########################################################################### # # File: mmcif_pdbx.dic # Date: Fri Jul 29 11:04:31 EDT 2005 # # Created from files in CVS module dict-mmcif_pdbx.dic unless noted: # mmcif_pdbx-header.dic # mmcif_pdbx-data.dic # mmcif_pdbx-def-1.dic # ../dict-mmcif_std/mmcif_std-def-2.dic # mmcif_pdbx-def-2.dic # mmcif_pdbx-def-3.dic # mmcif_pdbx-def-4.dic # mmcif_pdbx-def-5.dic # mmcif_pdbx-def-6.dic # ../dict-mmcif_iims/mmcif_iims-def-2.dic # mmcif_pdbx-def-8.dic # mmcif_pdbx-def-9.dic # mmcif_pdbx-def-10.dic # mmcif_pdbx-def-12.dic # ########################################################################### ########################################################################### # # File: mmcif_pdbx-header.dic # # PDB Exchange Data Dictionary # # This dictionary supplements the contents of the mmCIF data dictionary # with additional data items that may be required to store all of the # information currently included a Protein Data Bank (PDB) format data # file. Additional data items describing internal processing status # are also defined here. # # The mmCIF dictionary and this supplement provide the provisional # specifications for the data exchange protocol used by the wwPDB: # Resource Collaboratory for Structural Bioinformatics (RCSB) PDB, # Molecular Structure Database (MSD) Group/EBI, PDB Japan (PDBj) at # Osaka University. This dictionary also includes: data extensions # for structural genomics projects recommended by International Task # Force on Data Deposition and Archiving (including protein production), # NMR and 3D electron microscopy. # # # Header Section # ############################################################################## data_mmcif_pdbx.dic _datablock.id mmcif_pdbx.dic _datablock.description ; This data block holds the Protein Data Bank Exchange Data dictionary. ; _dictionary.title mmcif_pdbx.dic _dictionary.datablock_id mmcif_pdbx.dic _dictionary.version 1.019 # loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.001 2000-05-23 ; Initial revision based on RCSB local dictionaries and EBI database schema. J. Westbrook and J. Ionides ; 0.002 2000-06-06 ; Changes: (jdw) + Added items in refine_hist and exptl_crystal_grow ; 0.003 2000-10-16 ; Changes: (jdw) + Move enumerations to examples for: _pdbx_nmr_exptl.type _pdbx_nmr_ensemble.conformer_selection_criteria _pdbx_nmr_software.name _struct_keywords.pdbx_keywords + Added _atom_site_anisotrop.pdbx_auth_* items + Added _struct_mon_prot_cis.pdbx_ + Added _struct_conn.pdbx_ptnr3_auth_* items. ; 0.004 2000-10-24 ; Changes: (jdw) + Added optional timestamps to data items. + Repositioned parent items in PDBX_POLY_SEQ_SCHEME. ; 0.005 2000-10-25 ; Changes: (jdw) + drop category PDBX_DATABASE_REMARK ; 0.006 2000-10-26 ; Changes: (jdw) + Added _exptl_crystal_grow.rcsb_pH_range. + Added category PDBX_STRUCT_SHEET_HBOND to hold single hydrogen bond registration between beta sheet strands. ; 0.007 2000-11-09 ; Changes: (jdw) + Added mandatory codes for _exptl_crystal_grow.pdbx_details and _exptl_crystal_grow.pdbx_pH_range. + Added missing data types and category ids in category pdbx_struct_sheet_hbond. + Updated data type for atom name references to atcode. + Updated aliases for _refine.overall_SU_B and _refine.overall_SU_ML. + Trimmed line lengths > 80 characters. ; 0.008 2001-01-22 ; Changes: (jdw) + Added item _pdbx_database_status.dep_release_code_sequence ; 0.009 2001-03-02 ; Changes: (jdw) + Added missing mandatory codes and reset aliases for _diffrn_radiation.pdbx_wavelenth_list. ; 0.010 2001-04-18 ; Changes: (jdw) + Added missing _item_type.codes for _refine_hist.number_atoms_solvent _refine_hist.number_atoms_total _refine.overall_SU_B _refine.overall_SU_ML _refine.pdbx_overall_ESU_R + Added CCP4 data items output from REFMAC V5. ; 0.011 2001-06-14 ; Changes: (jdw) + Moved enumerations to examples for _pdbx_nmr_spectrometer.field_strength + _atom_site.pdb_auth_atom_name data type changed from code to atcode. ; 0.012 2001-06-28 ; Changes: (jdw) + _atom_site_anisotrop.pdbx_auth_* aliases corrected. + adjust regex for date:time type ; 0.013 2001-07-12 ; Changes: (jdw) + enumerations->examples for _pdbx_nmr_representative.selection_criteria and _pdbx_database_related.db_name. + add regex for int and float ranges ; 0.014 2002-02-28 ; Changes: (jdw) + Add items for NMR model and PDB insert code to GEOM_BOND, GEOM_ANGLE, GEOM_CONTACT, and GEOM_TORSION categories. ; 0.015 2002-05-22 ; Changes: (jdw) + Add PDBX_ENTITY_NONPOLY and fix missing data type codes. ; 0.016 2002-08-05 ; Changes: (jdw) + Add PDBX_AUDIT category. ; 0.017 2002-10-05 ; Changes: (jdw) + Final corrections of recommendations for NMR and X-ray deposition for structural genomics. ; 0.018 2003-07-07 ; Changes: (jdw) + Integrated protein production data items. ; 0.019 2003-09-21 ; Changes: (jdw/hy) + Added additional phasing items for PDB_EXTRACT. ; 0.020 2003-10-30 ; Changes: (jdw/zf) + Fix cases where category keys are not flagged as mandatory + Add category PDBX_AUDIT_AUTHOR ; 1.000 2004-04-22 ; Changes: (jdw) + New packaging and naming + Integrate 3d em definitions + Relax enumerations to comply with existing legacy data. + Version to 1.000 ; 1.001 2004-05-21 ; Changes: (jdw) + Fixed incorrect category in _pdbx_audit_author.address + Added _citation.pdbx_database_id_DOI + Fixed placement of _chem_comp.pdbx_align. Moved this item to _chem_comp_atom.pdbx_align ; 1.002 2004-06-09 ; Changes: (jdw) + Added categories PDBX_DOMAIN, PDBX_SEQUENCE_RANGE, PDBX_FEATURE_ENTRY, PDBX_FEATURE_ASSEMBLY, PDBX_FEATURE_DOMAIN, and PDBX_FEATURE_SEQUENCE_RANGE. ; 1.003 2004-06-16 ; Changes: (jdw) + Fix miscellaneous unresolved links. ; 1.004 2004-08-04 ; Changes: (jdw) + Fix many data type errors in phasing section. + Add pdbx_contact_author ; 1.005 2004-09-28 ; Changes: (zkf,jdw) + Add missing pdbx_contact_author.postal_code item + Add missing pdbx_contact_author.city item + Add missing pdbx_contact_author.state_province item + Add enumerations in pdbx_contact_author.id + Modify enumerations in pdbx_contact_author.role ; 1.006 2004-10-10 ; Changes: (jdw) + Update enumerations in cryo-em dictionary. ; 1.007 2004-11-02 ; Changes: (jdw) + added pdbx_entity_prod_protocol, pdbx_exptl_crystal_grow_sol, pdbx_exptl_crystal_grow_comp, and pdbx_exptl_crystal_cryo_treatment categories + relax enumerations in cryo-em dictionary. + remove upper-bound for refine.occupancy_max ; 1.008 2004-11-15 ; Changes: (jdw) + fix typo in category save frame name pdbx_exptl_crystal_grow_comp. ; 1.009 2005-01-13 ; Changes: (zkf) + add _pdbx_database_status.status_code_sf item + add _pdbx_database_status.date_of_sf_release item + add _pdbx_database_status.status_code_mr item + add _pdbx_database_status.date_of_mr_release item + add _pdbx_database_status.SG_entry item + add _entity_poly.pdbx_target_identifier item + add pdbx_SG_project category + fixed enumeration values for _software.language ; 1.010 2005-01-25 ; Changes: (jdw) + change mandatory doc for _pdbx_database_status.SG_entry + fix key in category pdbx_database_PDB_obs_spr ; 1.011 2005-03-08 ; Changes: (jdw) + Included extensions from mmCIF dictionary... Changes: (fzk) + add _pdbx_refine_tls_group.beg_auth_asym_id + add _pdbx_refine_tls_group.end_auth_asym_id + add enumeration values 'SGC' and 'NPPSFA' for _pdbx_SG_project.initial_of_center + add enumeration values 'Structural Genomics Consortium' and 'National Project on Protein Structural and Functional Analyses' for _pdbx_SG_project.full_name_of_center + fix _item_description.description for _entity_poly.pdbx_target_identifier ; 1.012 2005-03-29 ; Changes: (kh/jdw) + added preliminary set of extensions for macromolecular powder diffraction experiments, including: _pdbx_exptl_pd (category) _pdbx_exptl_pd.entry.id _pdbx_exptl_pd.spec_preparation_pH _pdbx_exptl_pd.spec_preparation_pH_range _pdbx_exptl_pd.spec_preparation _diffrn_radiation.pdbx_analyzer _refine.pdbx_pd_number_of_powder_patterns _refine.pdbx_pd_number_of_points _refine.pdbx_pd_meas_number_of_points _refine.pdbx_pd_proc_ls_prof_R_factor _refine.pdbx_pd_proc_ls_prof_wR_factor _refine.pdbx_pd_Marquardt_correlation_coeff _refine.pdbx_pd_Fsqrd_R_factor _refine.pdbx_pd_ls_matrix_band_width Changes: (fzk) removed 'National Project on Protein Structural and Functional Analyses' from _pdbx_SG_project.full_name_of_center, added 'National Project on Protein Structural and Functional Analyses' to _pdbx_SG_project.project_name ; 1.013 2005-04-05 ; Changes: (jdw) + Temporarily remove definitions from Image CIF dictionary + Added mandatory code for _cell.reciprocal_angle_beta + Added mandatory code for _pdbx_entity_nonpoly.entity_id + Fixed category attribute for _reflns_shell.pdbx_chi_squared + Changed mandatory code for _software.citation_id ; 1.014 2005-04-08 ; Changes: (jdw) + remove _struct_keywords.text from category key ; 1.015 2005-04-15 ; Changes: (jdw) + remove _entity_keywords.text from category key ; 1.016 2005-06-24 ; Changes: (jdw) + aliases repointed for items in category pdbx_database_remark + Added the following items: _diffrn_detector.pdbx_frames_total _diffrn_detector.pdbx_collection_time_total _refine.pdbx_ls_sigma_Fsqd _reflns.pdbx_Rmerge_I_all _reflns.pdbx_netI_over_sigmaI _reflns.pdbx_res_netI_over_av_sigmaI_2 _reflns.pdbx_res_netI_over_sigmaI_2 _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _struct_biol.pdbx_formula_weight _struct_biol.pdbx_formula_weight_method _struct_biol_gen.pdbx_PDB_order _phasing_MAD.pdbx_number_data_sets _phasing_MAD.pdbx_anom_scat_method _phasing_MIR.pdbx_number_derivatives _phasing_set.pdbx_temp_details + miscellaneous editorial changes in descriptions and enumerations. ; 1.017 2005-06-27 ; Changes: (BMcM) + added _reflns.threshold_expression and _publ_author.email + numerous minor changes to wordings of definitions to align with mmcif version 2.0.09 as released on International Tables G CD-ROM ; 1.018 2005-07-14 ; Changes: (jdw) + Added PDB_SOLN_SCATTER* definitions + Added _refln.pdbx_[F,I]_[minus,plus] and _refln.pdbx_[F,I]_[minus,plus]_sigma + Extend enumeration for _pdbx_database_status.status_code_sf ; 1.019 2005-07-21 ; Changes: (jdw) + Added _struct.pdbx_formula_weight and _struct.pdbx_formula_weight_method + Added _refln.pdbx_HL_A_iso, _refln.pdbx_HL_B_iso, _refln.pdbx_HL_C_iso, and _refln.pdbx_HL_D_iso + Added _phasing_set.pdbx_d_res_low/high _pdbx_phasing_MR.native_data_set_id + Added category pdbx_feature_monomer ; ### EOF mmcif_pdbx-header.dic ########################################################################### # # File: mmcif_pdbx-data.dic # # Protein Data Bank Exchange Data Dictionary # # # Data Section # # ########################################################################### ################## ## SUB_CATEGORY ## ################## loop_ _sub_category.id _sub_category.description 'cartesian_coordinate' ; The collection of x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. ; 'cartesian_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. ; 'fractional_coordinate' ; The collection of x, y, and z components of a position specified with reference to unit cell directions. ; 'fractional_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to unit cell directions. ; 'matrix' ; The collection of elements of a matrix. ; miller_index ; The collection of h, k, and l components of the Miller index of a reflection. ; 'cell_length' ; The collection of a, b, and c axis lengths of a unit cell. ; 'cell_length_esd' ; The collection of estimated standard deviations of the a, b, and c axis lengths of a unit cell. ; 'cell_angle' ; The collection of alpha, beta, and gamma angles of a unit cell. ; 'cell_angle_esd' ; The collection of estimated standard deviations of the alpha, beta, and gamma angles of a unit cell. ; 'mm_atom_site_auth_label' ; The collection of asym id, atom id, comp id and seq id components of an author's alternative specification for a macromolecular atom site. ; 'mm_atom_site_label' ; The collection of alt id, asym id, atom id, comp id and seq id components of the label for a macromolecular atom site. ; 'vector' ; The collection of elements of a vector. ; ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' . ; Categories that belong to the macromolecular dictionary. ; 'atom_group' 'inclusive_group' ; Categories that describe the properties of atoms. ; 'array_data_group' 'inclusive_group' ; Categories that describe array data. ; 'axis_group' 'inclusive_group' ; Categories that describe axes. ; 'audit_group' 'inclusive_group' ; Categories that describe dictionary maintenance and identification. ; 'cell_group' 'inclusive_group' ; Categories that describe the unit cell. ; 'chemical_group' 'inclusive_group' ; Categories that describe chemical properties and nomenclature. ; 'chem_comp_group' 'inclusive_group' ; Categories that describe components of chemical structure. ; 'chem_link_group' 'inclusive_group' ; Categories that describe links between components of chemical structure. ; 'citation_group' 'inclusive_group' ; Categories that provide bibliographic references. ; 'computing_group' 'inclusive_group' ; Categories that describe the computational details of the experiment. ; 'compliance_group' 'inclusive_group' ; Categories that are included in this dictionary specifically to comply with previous dictionaries. ; 'database_group' 'inclusive_group' ; Categories that hold references to entries in databases that contain related information. ; 'diffrn_group' 'inclusive_group' ; Categories that describe details of the diffraction experiment. ; 'em_group' 'inclusive_group' ; Categories that describe 3-dimensional electron microscopy. ; 'entity_group' 'inclusive_group' ; Categories that describe chemical entities. ; 'entry_group' 'inclusive_group' ; Categories that pertain to the entire data block. ; 'exptl_group' 'inclusive_group' ; Categories that hold details of the experimental conditions. ; 'geom_group' 'inclusive_group' ; Categories that hold details of molecular and crystal geometry. ; 'iucr_group' 'inclusive_group' ; Categories that are used for manuscript submission and internal processing by the staff of the International Union of Crystallography. ; 'pdb_group' 'inclusive_group' ; Categories that pertain to the file-format or data-processing codes used by the Protein Data Bank. ; 'phasing_group' 'inclusive_group' ; Categories that describe phasing. ; 'refine_group' 'inclusive_group' ; Categories that describe refinement. ; 'refln_group' 'inclusive_group' ; Categories that describe the details of reflection measurements. ; 'struct_group' 'inclusive_group' ; Categories that contain details about the crystallographic structure. ; 'symmetry_group' 'inclusive_group' ; Categories that describe symmetry information. ; 'pdbx_group' 'inclusive_group' ; Categories which are part of PDB data exchange protocol. ; 'pdbx_erf_group' 'inclusive_group' ; Categories which are used by RCSB PDB to store derived and computed data. ; 'ccp4_group' 'inclusive_group' ; Categories from the CCP4 harvest dictionary. ; 'ndb_group' 'inclusive_group' ; Categories which are used by the Nucleic Acid Database. ; 'rcsb_group' 'inclusive_group' ; Categories which are used internally by the RCSB PDB. ; 'protein_production_group' 'inclusive_group' ; Categories which describe the details of protein production. ; 'solution_scattering_group' 'inclusive_group' ; Categories which describe the details of solution scattering experiments. ; #################### ## ITEM_TYPE_LIST ## #################### # # # The regular expressions defined here are not compliant # with the POSIX 1003.2 standard as they include the # '\n' and '\t' special characters. These regular expressions # have been tested using version 0.12 of Richard Stallman's # GNU regular expression library in POSIX mode. # # # For some data items, a standard syntax is assumed. The syntax is # described for each data item in the dictionary, but is summarized here: # # Names: The family name(s) followed by a comma, precedes the first # name(s) or initial(s). # # Telephone numbers: # The international code is given in brackets and any extension # number is preceded by 'ext'. # # Dates: In the form yyyy-mm-dd. # ############################################################################## loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail code char '[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words ... ; ucode uchar '[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ... ; line char '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items ... ; uline uchar '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items (case insensitive)... ; text char '[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; text item types / multi-line text ... ; int numb '-?[0-9]+' ; int item types are the subset of numbers that are the negative or positive integers. ; float numb '-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?' ; float item types are the subset of numbers that are the floating numbers. ; name uchar '_[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+' ; name item types take the form... ; idname uchar '[_A-Za-z0-9]+' ; idname item types take the form... ; any char '.*' ; A catch all for items that may take any form... ; yyyy-mm-dd char '[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]' ; Standard format for CIF dates. ; uchar3 uchar '[+]?[A-Za-z0-9][A-Za-z0-9][A-Za-z0-9]' ; data item for 3 character codes ; uchar1 uchar '[+]?[A-Za-z0-9]' ; data item for 1 character codes ; symop char '([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])?' ; symop item types take the form n_klm, where n refers to the symmetry operation that is applied to the coordinates in the ATOM_SITE category identified by _atom_site_label. It must match a number given in _symmetry_equiv_pos_site_id. k, l, and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used. These translations (x,y,z) are related to (k,l,m) by k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; atcode char '[][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; Character data type for atom names ... ; yyyy-mm-dd:hh:mm char '[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9](-[0-9]?[0-9])?(:[0-9]?[0-9]:[0-9][0-9])?' ; Standard format for CIF dates with optional time stamp. ; fax uchar '[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ... ; phone uchar '[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ... ; email uchar '[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ... ; int-range numb '-?[0-9]+(--?[0-9]+)?' ; int item types are the subset of numbers that are the negative or positive integers with optional range. ; float-range numb '-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?(--?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?)?' ; int item types are the subset of numbers that are the floating numbers. ; code30 char '.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?' 'A string value, not allowed to exceed 30 characters.' # binary char ;\n--CIF-BINARY-FORMAT-SECTION--\n\ [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\ \n--CIF-BINARY-FORMAT-SECTION---- ; ; binary items are presented as MIME-like ascii-encoded sections in an imgCIF. In a CBF, raw octet streams are used to convey the same information. ; ##################### ## ITEM_UNITS_LIST ## ##################### loop_ _item_units_list.code _item_units_list.detail # 'metres' 'metres (metres)' 'centimetres' 'centimetres (metres * 10^( -2))' 'millimetres' 'millimetres (metres * 10^( -3))' 'nanometres' 'nanometres (metres * 10^( -9))' 'angstroms' 'angstroms (metres * 10^(-10))' 'picometres' 'picometres (metres * 10^(-12))' 'femtometres' 'femtometres (metres * 10^(-15))' # 'reciprocal_metres' 'reciprocal metres (metres^(-1))' 'reciprocal_centimetres' 'reciprocal centimetres ((metres * 10^( -2))^(-1))' 'reciprocal_millimetres' 'reciprocal millimetres ((metres * 10^( -3))^(-1))' 'reciprocal_nanometres' 'reciprocal nanometres ((metres * 10^( -9))^(-1))' 'reciprocal_angstroms' 'reciprocal angstroms ((metres * 10^(-10))^(-1))' 'reciprocal_picometres' 'reciprocal picometres ((metres * 10^(-12))^(-1))' # 'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2' 'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2' '8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2' 'picometres_squared' 'picometres squared (metres * 10^(-12))^2' # 'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3' 'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3' 'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3' # 'kilopascals' 'kilopascals' 'gigapascals' 'gigapascals' # 'hours' 'hours' 'minutes' 'minutes' 'seconds' 'seconds' 'microseconds' 'microseconds' # 'degrees' 'degrees (of arc)' # 'degrees_per_minute' 'degrees (of arc) per minute' # 'celsius' 'degrees (of temperature) Celsius' 'kelvins' 'degrees (of temperature) Kelvin' # 'electrons' 'electrons' # 'electrons_squared' 'electrons squared' # 'electrons_per_nanometres_cubed' ; electrons per nanometres cubed (electrons/(metres * 10^( -9))^(-3)) ; 'electrons_per_angstroms_cubed' ; electrons per angstroms cubed (electrons/(metres * 10^(-10))^(-3)) ; 'electrons_per_picometres_cubed' ; electrons per picometres cubed (electrons/(metres * 10^(-12))^(-3)) ; 'kilowatts' 'kilowatts' 'milliamperes' 'milliamperes' 'kilovolts' 'kilovolts' # 'arbitrary' ; arbitrary system of units. ; # 'angstroms_degrees' 'angstroms * degrees' # 'degrees_squared' 'degrees squared' # 'mg_per_ml' 'milliliter per milligram' # 'ml_per_min' 'milliliter per minute' # 'milliliters' 'liter / 1000' # 'milligrams' 'grams / 1000' # 'megadaltons' 'megadaltons' 'microns_squared' 'microns squared' 'microns' 'microns' # 'millimeters' 'millimeters' 'electrons_angstrom_squared' 'electrons square angstrom' 'electron_volts' 'electron volts' # 'mg/ml' 'mg per milliliter' 'millimolar' 'millimolar' 'megagrams_per_cubic_metre' 'megagrams per cubic metre' 'pixels_per_millimetre' 'pixels per millimetre' 'counts' 'counts' 'counts_per_photon' 'counts per photon' # loop_ _item_units_conversion.from_code _item_units_conversion.to_code _item_units_conversion.operator _item_units_conversion.factor ### 'metres' 'centimetres' '*' 1.0E+02 'metres' 'millimetres' '*' 1.0E+03 'metres' 'nanometres' '*' 1.0E+09 'metres' 'angstroms' '*' 1.0E+10 'metres' 'picometres' '*' 1.0E+12 'metres' 'femtometres' '*' 1.0E+15 'centimetres' 'millimetres' '*' 1.0E+01 'centimetres' 'nanometres' '*' 1.0E+07 'centimetres' 'angstroms' '*' 1.0E+08 'centimetres' 'picometres' '*' 1.0E+10 'centimetres' 'femtometres' '*' 1.0E+13 # 'millimetres' 'centimetres' '*' 1.0E-01 'millimetres' 'nanometres' '*' 1.0E+06 'millimetres' 'angstroms' '*' 1.0E+07 'millimetres' 'picometres' '*' 1.0E+09 'millimetres' 'femtometres' '*' 1.0E+12 # 'nanometres' 'centimetres' '*' 1.0E-07 'nanometres' 'millimetres' '*' 1.0E-06 'nanometres' 'angstroms' '*' 1.0E+01 'nanometres' 'picometres' '*' 1.0E+03 'nanometres' 'femtometres' '*' 1.0E+06 # 'angstroms' 'centimetres' '*' 1.0E-08 'angstroms' 'millimetres' '*' 1.0E-07 'angstroms' 'nanometres' '*' 1.0E-01 'angstroms' 'picometres' '*' 1.0E+02 'angstroms' 'femtometres' '*' 1.0E+05 # 'picometres' 'centimetres' '*' 1.0E-10 'picometres' 'millimetres' '*' 1.0E-09 'picometres' 'nanometres' '*' 1.0E-03 'picometres' 'angstroms' '*' 1.0E-02 'picometres' 'femtometres' '*' 1.0E+03 # 'femtometres' 'centimetres' '*' 1.0E-13 'femtometres' 'millimetres' '*' 1.0E-12 'femtometres' 'nanometres' '*' 1.0E-06 'femtometres' 'angstroms' '*' 1.0E-05 'femtometres' 'picometres' '*' 1.0E-03 ### 'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01 'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07 'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08 'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10 # 'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01 'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06 'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07 'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09 # 'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07 'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06 'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01 'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03 # 'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08 'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07 'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01 'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02 # 'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10 'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09 'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03 'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01 ### 'nanometres_squared' 'angstroms_squared' '*' 1.0E+02 'nanometres_squared' 'picometres_squared' '*' 1.0E+06 # 'angstroms_squared' 'nanometres_squared' '*' 1.0E-02 'angstroms_squared' 'picometres_squared' '*' 1.0E+04 'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568 # 'picometres_squared' 'nanometres_squared' '*' 1.0E-06 'picometres_squared' 'angstroms_squared' '*' 1.0E-04 ### 'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03 'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09 # 'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03 'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06 # 'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09 'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06 ### 'kilopascals' 'gigapascals' '*' 1.0E-06 'gigapascals' 'kilopascals' '*' 1.0E+06 ### 'hours' 'minutes' '*' 6.0E+01 'hours' 'seconds' '*' 3.6E+03 'hours' 'microseconds' '*' 3.6E+09 # 'minutes' 'hours' '/' 6.0E+01 'minutes' 'seconds' '*' 6.0E+01 'minutes' 'microseconds' '*' 6.0E+07 # 'seconds' 'hours' '/' 3.6E+03 'seconds' 'minutes' '/' 6.0E+01 'seconds' 'microseconds' '*' 1.0E+06 # 'microseconds' 'hours' '/' 3.6E+09 'microseconds' 'minutes' '/' 6.0E+07 'microseconds' 'seconds' '/' 1.0E+06 ### 'celsius' 'kelvins' '-' 273.0 'kelvins' 'celsius' '+' 273.0 ### 'electrons_per_nanometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E+03 'electrons_per_nanometres_cubed' 'electrons_per_picometres_cubed' '*' 1.0E+09 # 'electrons_per_angstroms_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E-03 'electrons_per_angstroms_cubed' 'electrons_per_picometres_cubed' '*' 1.0E+06 # 'electrons_per_picometres_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E-09 'electrons_per_picometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E-06 ### ### EOF mmcif_pdbx-data.dic ########################################################################### # # File: mmcif_std-def-1.dic # # mmCIF Data Dictionary (standard defintions) # # This data dictionary contains the standard mmCIF data definitions. # # Defintion Section 1 # # ########################################################################### ############### ## ATOM_SITE ## ############### save_atom_site _category.description ; Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. ; _category.id atom_site _category.mandatory_code no _category_key.name '_atom_site.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_site.group_PDB _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.footnote_id _atom_site.auth_seq_id _atom_site.id ATOM N N VAL A 11 . 25.369 30.691 11.795 1.00 17.93 . 11 1 ATOM C CA VAL A 11 . 25.970 31.965 12.332 1.00 17.75 . 11 2 ATOM C C VAL A 11 . 25.569 32.010 13.808 1.00 17.83 . 11 3 ATOM O O VAL A 11 . 24.735 31.190 14.167 1.00 17.53 . 11 4 ATOM C CB VAL A 11 . 25.379 33.146 11.540 1.00 17.66 . 11 5 ATOM C CG1 VAL A 11 . 25.584 33.034 10.030 1.00 18.86 . 11 6 ATOM C CG2 VAL A 11 . 23.933 33.309 11.872 1.00 17.12 . 11 7 ATOM N N THR A 12 . 26.095 32.930 14.590 1.00 18.97 4 12 8 ATOM C CA THR A 12 . 25.734 32.995 16.032 1.00 19.80 4 12 9 ATOM C C THR A 12 . 24.695 34.106 16.113 1.00 20.92 4 12 10 ATOM O O THR A 12 . 24.869 35.118 15.421 1.00 21.84 4 12 11 ATOM C CB THR A 12 . 26.911 33.346 17.018 1.00 20.51 4 12 12 ATOM O OG1 THR A 12 3 27.946 33.921 16.183 0.50 20.29 4 12 13 ATOM O OG1 THR A 12 4 27.769 32.142 17.103 0.50 20.59 4 12 14 ATOM C CG2 THR A 12 3 27.418 32.181 17.878 0.50 20.47 4 12 15 ATOM C CG2 THR A 12 4 26.489 33.778 18.426 0.50 20.00 4 12 16 ATOM N N ILE A 13 . 23.664 33.855 16.884 1.00 22.08 . 13 17 ATOM C CA ILE A 13 . 22.623 34.850 17.093 1.00 23.44 . 13 18 ATOM C C ILE A 13 . 22.657 35.113 18.610 1.00 25.77 . 13 19 ATOM O O ILE A 13 . 23.123 34.250 19.406 1.00 26.28 . 13 20 ATOM C CB ILE A 13 . 21.236 34.463 16.492 1.00 22.67 . 13 21 ATOM C CG1 ILE A 13 . 20.478 33.469 17.371 1.00 22.14 . 13 22 ATOM C CG2 ILE A 13 . 21.357 33.986 15.016 1.00 21.75 . 13 23 # - - - - data truncated for brevity - - - - HETATM C C1 APS C . 1 4.171 29.012 7.116 0.58 17.27 1 300 101 HETATM C C2 APS C . 1 4.949 27.758 6.793 0.58 16.95 1 300 102 HETATM O O3 APS C . 1 4.800 26.678 7.393 0.58 16.85 1 300 103 HETATM N N4 APS C . 1 5.930 27.841 5.869 0.58 16.43 1 300 104 # - - - - data truncated for brevity - - - - ; save_ save__atom_site.aniso_B[1][1] _item_description.description ; The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][1]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][1]_esd' associated_esd '_atom_site.aniso_U[1][1]' conversion_constant '_atom_site_anisotrop.U[1][1]' conversion_constant '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][1]. ; _item.name '_atom_site.aniso_B[1][1]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][1]' associated_value '_atom_site.aniso_U[1][1]_esd' conversion_constant '_atom_site_anisotrop.U[1][1]_esd' conversion_constant '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][2] _item_description.description ; The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][2]_esd' associated_esd '_atom_site.aniso_U[1][2]' conversion_constant '_atom_site_anisotrop.U[1][2]' conversion_constant '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][2]. ; _item.name '_atom_site.aniso_B[1][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][2]' associated_value '_atom_site.aniso_U[1][2]_esd' conversion_constant '_atom_site_anisotrop.U[1][2]_esd' conversion_constant '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][3] _item_description.description ; The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][3]_esd' associated_esd '_atom_site.aniso_U[1][3]' conversion_constant '_atom_site_anisotrop.U[1][3]' conversion_constant '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][3]. ; _item.name '_atom_site.aniso_B[1][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][3]' associated_value '_atom_site.aniso_U[1][3]_esd' conversion_constant '_atom_site_anisotrop.U[1][3]_esd' conversion_constant '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][2] _item_description.description ; The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[2][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][2]_esd' associated_esd '_atom_site.aniso_U[2][2]' conversion_constant '_atom_site_anisotrop.U[2][2]' conversion_constant '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[2][2]. ; _item.name '_atom_site.aniso_B[2][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][2]' associated_value '_atom_site.aniso_U[2][2]_esd' conversion_constant '_atom_site_anisotrop.U[2][2]_esd' conversion_constant '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][3] _item_description.description ; The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[2][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][3]_esd' associated_esd '_atom_site.aniso_U[2][3]' conversion_constant '_atom_site_anisotrop.U[2][3]' conversion_constant '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[2][3]. ; _item.name '_atom_site.aniso_B[2][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][3]' associated_value '_atom_site.aniso_U[2][3]_esd' conversion_constant '_atom_site_anisotrop.U[2][3]_esd' conversion_constant '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[3][3] _item_description.description ; The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[3][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[3][3]_esd' associated_esd '_atom_site.aniso_U[3][3]' conversion_constant '_atom_site_anisotrop.U[3][3]' conversion_constant '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[3][3]. ; _item.name '_atom_site.aniso_B[3][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[3][3]' associated_value '_atom_site.aniso_U[3][3]_esd' conversion_constant '_atom_site_anisotrop.U[3][3]_esd' conversion_constant '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_ratio _item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site.aniso_ratio' _item.category_id atom_site _item.mandatory_code no _item_related.related_name '_atom_site_anisotrop.ratio' _item_related.function_code alternate_exclusive loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__atom_site.aniso_U[1][1] _item_description.description ; The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][1]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][1]_esd' associated_esd '_atom_site.aniso_B[1][1]' conversion_constant '_atom_site_anisotrop.B[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][1]. ; _item.name '_atom_site.aniso_U[1][1]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][1]' associated_value '_atom_site.aniso_B[1][1]_esd' conversion_constant '_atom_site_anisotrop.B[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][2] _item_description.description ; The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][2]_esd' associated_esd '_atom_site.aniso_B[1][2]' conversion_constant '_atom_site_anisotrop.B[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][2]. ; _item.name '_atom_site.aniso_U[1][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][2]' associated_value '_atom_site.aniso_B[1][2]_esd' conversion_constant '_atom_site_anisotrop.B[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][3] _item_description.description ; The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][3]_esd' associated_esd '_atom_site.aniso_B[1][3]' conversion_constant '_atom_site_anisotrop.B[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][3]. ; _item.name '_atom_site.aniso_U[1][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][3]' associated_value '_atom_site.aniso_B[1][3]_esd' conversion_constant '_atom_site_anisotrop.B[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][2] _item_description.description ; The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[2][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][2]_esd' associated_esd '_atom_site.aniso_B[2][2]' conversion_constant '_atom_site_anisotrop.B[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[2][2]. ; _item.name '_atom_site.aniso_U[2][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][2]' associated_value '_atom_site.aniso_B[2][2]_esd' conversion_constant '_atom_site_anisotrop.B[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][3] _item_description.description ; The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[2][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][3]_esd' associated_esd '_atom_site.aniso_B[2][3]' conversion_constant '_atom_site_anisotrop.B[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[2][3]. ; _item.name '_atom_site.aniso_U[2][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][3]' associated_value '_atom_site.aniso_B[2][3]_esd' conversion_constant '_atom_site_anisotrop.B[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[3][3] _item_description.description ; The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[3][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[3][3]_esd' associated_esd '_atom_site.aniso_B[3][3]' conversion_constant '_atom_site_anisotrop.B[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[3][3]. ; _item.name '_atom_site.aniso_U[3][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[3][3]' associated_value '_atom_site.aniso_B[3][3]_esd' conversion_constant '_atom_site_anisotrop.B[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.attached_hydrogens _item_description.description ; The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given. ; _item.name '_atom_site.attached_hydrogens' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_attached_hydrogens' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 0 0 0 _item_type.code int loop_ _item_examples.case _item_examples.detail 2 'water oxygen' 1 'hydroxyl oxygen' 4 'ammonium nitrogen' save_ save__atom_site.auth_asym_id _item_description.description ; An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_asym_id' atom_site yes '_geom_angle.atom_site_auth_asym_id_1' geom_angle no '_geom_angle.atom_site_auth_asym_id_2' geom_angle no '_geom_angle.atom_site_auth_asym_id_3' geom_angle no '_geom_bond.atom_site_auth_asym_id_1' geom_bond no '_geom_bond.atom_site_auth_asym_id_2' geom_bond no '_geom_contact.atom_site_auth_asym_id_1' geom_contact no '_geom_contact.atom_site_auth_asym_id_2' geom_contact no '_geom_hbond.atom_site_auth_asym_id_A' geom_hbond no '_geom_hbond.atom_site_auth_asym_id_D' geom_hbond no '_geom_hbond.atom_site_auth_asym_id_H' geom_hbond no '_geom_torsion.atom_site_auth_asym_id_1' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_2' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_3' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_4' geom_torsion no '_struct_conf.beg_auth_asym_id' struct_conf no '_struct_conf.end_auth_asym_id' struct_conf no '_struct_conn.ptnr1_auth_asym_id' struct_conn no '_struct_conn.ptnr2_auth_asym_id' struct_conn no '_struct_mon_nucl.auth_asym_id' struct_mon_nucl no '_struct_mon_prot.auth_asym_id' struct_mon_prot no '_struct_mon_prot_cis.auth_asym_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_asym_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_asym_id' struct_ncs_dom_lim no '_struct_sheet_range.beg_auth_asym_id' struct_sheet_range no '_struct_sheet_range.end_auth_asym_id' struct_sheet_range no '_struct_site_gen.auth_asym_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_angle.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_angle.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id' '_geom_bond.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_bond.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_contact.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_contact.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_A' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_D' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_H' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_4' '_atom_site.auth_asym_id' '_struct_conf.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conf.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conn.ptnr1_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conn.ptnr2_auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_nucl.auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_prot.auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_prot_cis.auth_asym_id' '_atom_site.auth_asym_id' '_struct_ncs_dom_lim.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_ncs_dom_lim.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_sheet_range.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_sheet_range.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_site_gen.auth_asym_id' '_atom_site.auth_asym_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_atom_id _item_description.description ; An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_atom_id' atom_site no '_geom_angle.atom_site_auth_atom_id_1' geom_angle no '_geom_angle.atom_site_auth_atom_id_2' geom_angle no '_geom_angle.atom_site_auth_atom_id_3' geom_angle no '_geom_bond.atom_site_auth_atom_id_1' geom_bond no '_geom_bond.atom_site_auth_atom_id_2' geom_bond no '_geom_contact.atom_site_auth_atom_id_1' geom_contact no '_geom_contact.atom_site_auth_atom_id_2' geom_contact no '_geom_hbond.atom_site_auth_atom_id_A' geom_hbond no '_geom_hbond.atom_site_auth_atom_id_D' geom_hbond no '_geom_hbond.atom_site_auth_atom_id_H' geom_hbond no '_geom_torsion.atom_site_auth_atom_id_1' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_2' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_3' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_4' geom_torsion no '_struct_conn.ptnr1_auth_atom_id' struct_conn no '_struct_conn.ptnr2_auth_atom_id' struct_conn no '_struct_sheet_hbond.range_1_beg_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_1_end_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_beg_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_end_auth_atom_id' struct_sheet_hbond no '_struct_site_gen.auth_atom_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_angle.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_angle.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id' '_geom_bond.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_bond.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_contact.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_contact.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_A' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_D' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_H' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_4' '_atom_site.auth_atom_id' '_struct_conn.ptnr1_auth_atom_id' '_atom_site.auth_atom_id' '_struct_conn.ptnr2_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_1_beg_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_1_end_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_2_beg_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_2_end_auth_atom_id' '_atom_site.auth_atom_id' '_struct_site_gen.auth_atom_id' '_atom_site.auth_atom_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code atcode save_ save__atom_site.auth_comp_id _item_description.description ; An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_comp_id' atom_site no '_geom_angle.atom_site_auth_comp_id_1' geom_angle no '_geom_angle.atom_site_auth_comp_id_2' geom_angle no '_geom_angle.atom_site_auth_comp_id_3' geom_angle no '_geom_bond.atom_site_auth_comp_id_1' geom_bond no '_geom_bond.atom_site_auth_comp_id_2' geom_bond no '_geom_contact.atom_site_auth_comp_id_1' geom_contact no '_geom_contact.atom_site_auth_comp_id_2' geom_contact no '_geom_hbond.atom_site_auth_comp_id_A' geom_hbond no '_geom_hbond.atom_site_auth_comp_id_D' geom_hbond no '_geom_hbond.atom_site_auth_comp_id_H' geom_hbond no '_geom_torsion.atom_site_auth_comp_id_1' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_2' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_3' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_4' geom_torsion no '_struct_conf.beg_auth_comp_id' struct_conf no '_struct_conf.end_auth_comp_id' struct_conf no '_struct_conn.ptnr1_auth_comp_id' struct_conn no '_struct_conn.ptnr2_auth_comp_id' struct_conn no '_struct_mon_nucl.auth_comp_id' struct_mon_nucl no '_struct_mon_prot.auth_comp_id' struct_mon_prot no '_struct_mon_prot_cis.auth_comp_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_comp_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_comp_id' struct_ncs_dom_lim no '_struct_sheet_range.beg_auth_comp_id' struct_sheet_range no '_struct_sheet_range.end_auth_comp_id' struct_sheet_range no '_struct_site_gen.auth_comp_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_angle.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_angle.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id' '_geom_bond.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_bond.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_contact.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_contact.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_A' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_D' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_H' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_4' '_atom_site.auth_comp_id' '_struct_conf.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conf.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conn.ptnr1_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conn.ptnr2_auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_nucl.auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_prot.auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_prot_cis.auth_comp_id' '_atom_site.auth_comp_id' '_struct_ncs_dom_lim.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_ncs_dom_lim.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_sheet_range.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_sheet_range.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_site_gen.auth_comp_id' '_atom_site.auth_comp_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_seq_id _item_description.description ; An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of _atom_site.label_seq_id. The value of _atom_site.label_seq_id is required to be a sequential list of positive integers. The author may assign values to _atom_site.auth_seq_id in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_seq_id' atom_site no '_geom_angle.atom_site_auth_seq_id_1' geom_angle no '_geom_angle.atom_site_auth_seq_id_2' geom_angle no '_geom_angle.atom_site_auth_seq_id_3' geom_angle no '_geom_bond.atom_site_auth_seq_id_1' geom_bond no '_geom_bond.atom_site_auth_seq_id_2' geom_bond no '_geom_contact.atom_site_auth_seq_id_1' geom_contact no '_geom_contact.atom_site_auth_seq_id_2' geom_contact no '_geom_hbond.atom_site_auth_seq_id_A' geom_hbond no '_geom_hbond.atom_site_auth_seq_id_D' geom_hbond no '_geom_hbond.atom_site_auth_seq_id_H' geom_hbond no '_geom_torsion.atom_site_auth_seq_id_1' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_2' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_3' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_4' geom_torsion no '_struct_conf.beg_auth_seq_id' struct_conf no '_struct_conf.end_auth_seq_id' struct_conf no '_struct_conn.ptnr1_auth_seq_id' struct_conn no '_struct_conn.ptnr2_auth_seq_id' struct_conn no '_struct_mon_nucl.auth_seq_id' struct_mon_nucl no '_struct_mon_prot.auth_seq_id' struct_mon_prot no '_struct_mon_prot_cis.auth_seq_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_seq_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_seq_id' struct_ncs_dom_lim no '_struct_sheet_hbond.range_1_beg_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_1_end_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_beg_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_end_auth_seq_id' struct_sheet_hbond no '_struct_sheet_range.beg_auth_seq_id' struct_sheet_range no '_struct_sheet_range.end_auth_seq_id' struct_sheet_range no '_struct_site_gen.auth_seq_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_angle.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_angle.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id' '_geom_bond.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_bond.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_contact.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_contact.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_A' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_D' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_H' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_4' '_atom_site.auth_seq_id' '_struct_conf.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conf.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conn.ptnr1_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conn.ptnr2_auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_nucl.auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_prot.auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_prot_cis.auth_seq_id' '_atom_site.auth_seq_id' '_struct_ncs_dom_lim.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_ncs_dom_lim.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_1_beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_1_end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_2_beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_2_end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_range.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_range.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_site_gen.auth_seq_id' '_atom_site.auth_seq_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.B_equiv_geom_mean _item_description.description ; Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~eq~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.B_equiv_geom_mean' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_B_equiv_geom_mean' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_equiv_geom_mean_esd' associated_esd '_atom_site.U_equiv_geom_mean' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_equiv_geom_mean_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.B_equiv_geom_mean. ; _item.name '_atom_site.B_equiv_geom_mean_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_equiv_geom_mean' associated_value '_atom_site.U_equiv_geom_mean' conversion_constant _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_iso_or_equiv _item_description.description ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.B_iso_or_equiv' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_B_iso_or_equiv' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_iso_or_equiv_esd' associated_esd '_atom_site.U_iso_or_equiv' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_iso_or_equiv_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.B_iso_or_equiv. ; _item.name '_atom_site.B_iso_or_equiv_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_iso_or_equiv' associated_value '_atom_site.U_iso_or_equiv_esd' conversion_constant _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.calc_attached_atom _item_description.description ; The _atom_site.id of the atom site to which the 'geometry-calculated' atom site is attached. ; _item.name '_atom_site.calc_attached_atom' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_attached_atom' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__atom_site.calc_flag _item_description.description ; A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. The abbreviation 'c' may be used in place of 'calc'. ; _item.name '_atom_site.calc_flag' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value d _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail d 'determined from experimental measurements' calc 'calculated from molecular geometry' c 'abbreviation for "calc"' dum 'dummy site with meaningless coordinates' save_ save__atom_site.Cartn_x _item_description.description ; The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_x' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_x' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_y' '_atom_site.Cartn_z' _item_related.related_name '_atom_site.Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_x. ; _item.name '_atom_site.Cartn_x_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_y_esd' '_atom_site.Cartn_z_esd' _item_related.related_name '_atom_site.Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.Cartn_y _item_description.description ; The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_y' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_y' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_z' _item_related.related_name '_atom_site.Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_y. ; _item.name '_atom_site.Cartn_y_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x_esd' '_atom_site.Cartn_z_esd' _item_related.related_name '_atom_site.Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.Cartn_z _item_description.description ; The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_z' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_z' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_y' _item_related.related_name '_atom_site.Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_z. ; _item.name '_atom_site.Cartn_z_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x_esd' '_atom_site.Cartn_y_esd' _item_related.related_name '_atom_site.Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.chemical_conn_number _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_atom_site.chemical_conn_number' _item.mandatory_code no _item_aliases.alias_name '_atom_site_chemical_conn_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site.constraints _item_description.description ; A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_constraints. ; _item.name '_atom_site.constraints' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_constraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'pop=1.0-pop(Zn3)' save_ save__atom_site.details _item_description.description ; A description of special aspects of this site. See also _atom_site.refinement_flags. ; _item.name '_atom_site.details' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Ag/Si disordered' save_ save__atom_site.disorder_assembly _item_description.description ; A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site.disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_site.disorder_assembly' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_disorder_assembly' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__atom_site.disorder_group _item_description.description ; A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_site.disorder_group' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_disorder_group' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value . _item_type.code code save_ save__atom_site.footnote_id _item_description.description ; The value of _atom_site.footnote_id must match an ID specified by _atom_sites_footnote.id in the ATOM_SITES_FOOTNOTE list. ; _item.name '_atom_site.footnote_id' _item.mandatory_code no save_ save__atom_site.fract_x _item_description.description ; The x coordinate of the atom-site position specified as a fraction of _cell.length_a. ; _item.name '_atom_site.fract_x' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_x' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.fract_y' '_atom_site.fract_z' _item_related.related_name '_atom_site.fract_x_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.fract_x. ; _item.name '_atom_site.fract_x_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_y_esd' '_atom_site.fract_z_esd' _item_related.related_name '_atom_site.fract_x' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.fract_y _item_description.description ; The y coordinate of the atom-site position specified as a fraction of _cell.length_b. ; _item.name '_atom_site.fract_y' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_y' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_z' _item_related.related_name '_atom_site.fract_y_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.fract_y. ; _item.name '_atom_site.fract_y_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_z_esd' _item_related.related_name '_atom_site.fract_y' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.fract_z _item_description.description ; The z coordinate of the atom-site position specified as a fraction of _cell.length_c. ; _item.name '_atom_site.fract_z' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_z' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_y' _item_related.related_name '_atom_site.fract_z_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.fract_z. ; _item.name '_atom_site.fract_z_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_y_esd' _item_related.related_name '_atom_site.fract_z' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.group_PDB _item_description.description ; The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; _item.name '_atom_site.group_PDB' _item.category_id atom_site _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value ATOM HETATM save_ save__atom_site.id _item_description.description ; The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and _atom_site.label_seq_id. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to _atom_site.id. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.id' atom_site yes '_atom_site_anisotrop.id' atom_site_anisotrop yes '_geom_angle.atom_site_id_1' geom_angle yes '_geom_angle.atom_site_id_2' geom_angle yes '_geom_angle.atom_site_id_3' geom_angle yes '_geom_bond.atom_site_id_1' geom_bond yes '_geom_bond.atom_site_id_2' geom_bond yes '_geom_contact.atom_site_id_1' geom_contact yes '_geom_contact.atom_site_id_2' geom_contact yes '_geom_hbond.atom_site_id_A' geom_hbond yes '_geom_hbond.atom_site_id_D' geom_hbond yes '_geom_hbond.atom_site_id_H' geom_hbond yes '_geom_torsion.atom_site_id_1' geom_torsion yes '_geom_torsion.atom_site_id_2' geom_torsion yes '_geom_torsion.atom_site_id_3' geom_torsion yes '_geom_torsion.atom_site_id_4' geom_torsion yes _item_aliases.alias_name '_atom_site_label' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site_anisotrop.id' '_atom_site.id' '_geom_angle.atom_site_id_1' '_atom_site.id' '_geom_angle.atom_site_id_2' '_atom_site.id' '_geom_angle.atom_site_id_3' '_atom_site.id' '_geom_bond.atom_site_id_1' '_atom_site.id' '_geom_bond.atom_site_id_2' '_atom_site.id' '_geom_contact.atom_site_id_1' '_atom_site.id' '_geom_contact.atom_site_id_2' '_atom_site.id' '_geom_hbond.atom_site_id_A' '_atom_site.id' '_geom_hbond.atom_site_id_D' '_atom_site.id' '_geom_hbond.atom_site_id_H' '_atom_site.id' '_geom_torsion.atom_site_id_1' '_atom_site.id' '_geom_torsion.atom_site_id_2' '_atom_site.id' '_geom_torsion.atom_site_id_3' '_atom_site.id' '_geom_torsion.atom_site_id_4' '_atom_site.id' _item_type.code code loop_ _item_examples.case '5' 'C12' 'Ca3g28' 'Fe3+17' 'H*251' 'boron2a' 'C_a_phe_83_a_0' 'Zn_Zn_301_A_0' save_ save__atom_site.label_alt_id _item_description.description ; A component of the identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_atom_site.label_alt_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_asym_id _item_description.description ; A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_atom_site.label_asym_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_atom_id _item_description.description ; A component of the identifier for this atom site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_atom_site.label_atom_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_comp_id _item_description.description ; A component of the identifier for this atom site. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_atom_site.label_comp_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_atom_site.label_entity_id' _item.mandatory_code yes save_ save__atom_site.label_seq_id _item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_atom_site.label_seq_id' _item.mandatory_code yes save_ save__atom_site.occupancy _item_description.description ; The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. ; _item.name '_atom_site.occupancy' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_occupancy' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1.0 # JDW 17-Apr-2003 - Unsupportable restriction. # loop_ # _item_range.maximum # _item_range.minimum 1.0 1.0 # 1.0 0.0 # 0.0 0.0 _item_related.related_name '_atom_site.occupancy_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__atom_site.occupancy_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.occupancy. ; _item.name '_atom_site.occupancy_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_atom_site.occupancy' _item_related.function_code associated_value _item_type.code float save_ #save__atom_site.refinement_flags # _item_description.description #; A concatenated series of single-letter codes which indicate the # refinement restraints or constraints applied to this site. #; # _item.name '_atom_site.refinement_flags' # _item.category_id atom_site # _item.mandatory_code no # _item_aliases.alias_name '_atom_site_refinement_flags' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # _item_type.code ucode # loop_ # _item_enumeration.value # _item_enumeration.detail . # 'no refinement constraints' # S # 'special-position constraint on site' # G # 'rigid-group refinement of site' # R # 'riding atom site attached to non-riding atom' # D # 'distance or angle restraint on site' # T # 'thermal displacement constraints' # U # 'Uiso or Uij restraint (rigid bond)' # P # 'partial occupancy constraint' # save_ save__atom_site.restraints _item_description.description ; A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_restraints. ; _item.name '_atom_site.restraints' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_restraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'restrained to planar ring' save_ save__atom_site.symmetry_multiplicity _item_description.description ; The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002). ; _item.name '_atom_site.symmetry_multiplicity' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_symmetry_multiplicity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 192 192 192 1 1 1 _item_type.code int save_ save__atom_site.thermal_displace_type _item_description.description ; A standard code used to describe the type of atomic displacement parameters used for the site. ; _item.name '_atom_site.thermal_displace_type' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_thermal_displace_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' save_ save__atom_site.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_atom_site.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site.U_equiv_geom_mean _item_description.description ; Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~eq~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^ ; _item.name '_atom_site.U_equiv_geom_mean' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_U_equiv_geom_mean' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 10.0 10.0 10.0 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_equiv_geom_mean_esd' associated_esd '_atom_site.B_equiv_geom_mean' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.U_equiv_geom_mean_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.U_equiv_geom_mean. ; _item.name '_atom_site.U_equiv_geom_mean_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_equiv_geom_mean' associated_value '_atom_site.B_equiv_geom_mean' conversion_constant _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.U_iso_or_equiv _item_description.description ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters. U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. ; _item.name '_atom_site.U_iso_or_equiv' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_U_iso_or_equiv' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 10.0 10.0 10.0 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_iso_or_equiv_esd' associated_esd '_atom_site.B_iso_or_equiv' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.U_iso_or_equiv_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.U_iso_or_equiv. ; _item.name '_atom_site.U_iso_or_equiv_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_iso_or_equiv' associated_value '_atom_site.B_iso_or_equiv_esd' conversion_constant _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.Wyckoff_symbol _item_description.description ; The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002). ; _item.name '_atom_site.Wyckoff_symbol' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Wyckoff_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ######################### ## ATOM_SITE_ANISOTROP ## ######################### save_atom_site_anisotrop _category.description ; Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. ; _category.id atom_site_anisotrop _category.mandatory_code no _category_key.name '_atom_site_anisotrop.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson & Kim [Acta Cryst. (1985), B41, 255-262]. ; ; loop_ _atom_site_anisotrop.id _atom_site_anisotrop.type_symbol _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[1][2] _atom_site_anisotrop.U[1][3] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[2][3] _atom_site_anisotrop.U[3][3] 1 O 8642 4866 7299 -342 -258 -1427 2 C 5174 4871 6243 -1885 -2051 -1377 3 C 6202 5020 4395 -1130 -556 -632 4 O 4224 4700 5046 1105 -161 345 5 C 8684 4688 4171 -1850 -433 -292 6 O 11226 5255 3532 -341 2685 1328 7 C 10214 2428 5614 -2610 -1940 902 8 C 4590 3488 5827 751 -770 986 9 N 5014 4434 3447 -17 -1593 539 # ---- abbreviated ---- ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_site_anisotrop.B[1][1] _item_description.description ; The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][1]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][1]_esd' associated_esd '_atom_site.aniso_U[1][1]' conversion_constant '_atom_site_anisotrop.U[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][1]. ; _item.name '_atom_site_anisotrop.B[1][1]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][1]' associated_value '_atom_site.aniso_U[1][1]_esd' conversion_constant '_atom_site_anisotrop.U[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][2] _item_description.description ; The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][2]_esd' associated_esd '_atom_site.aniso_U[1][2]' conversion_constant '_atom_site_anisotrop.U[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][2]. ; _item.name '_atom_site_anisotrop.B[1][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][2]' associated_value '_atom_site.aniso_U[1][2]_esd' conversion_constant '_atom_site_anisotrop.U[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][3] _item_description.description ; The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][3]_esd' associated_esd '_atom_site.aniso_U[1][3]' conversion_constant '_atom_site_anisotrop.U[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][3]. ; _item.name '_atom_site_anisotrop.B[1][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][3]' associated_value '_atom_site.aniso_U[1][3]_esd' conversion_constant '_atom_site_anisotrop.U[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][2] _item_description.description ; The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[2][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][2]_esd' associated_esd '_atom_site.aniso_U[2][2]' conversion_constant '_atom_site_anisotrop.U[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[2][2]. ; _item.name '_atom_site_anisotrop.B[2][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][2]' associated_value '_atom_site.aniso_U[2][2]_esd' conversion_constant '_atom_site_anisotrop.U[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][3] _item_description.description ; The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[2][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][3]_esd' associated_esd '_atom_site.aniso_U[2][3]' conversion_constant '_atom_site_anisotrop.U[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[2][3]. ; _item.name '_atom_site_anisotrop.B[2][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][3]' associated_value '_atom_site.aniso_U[2][3]_esd' conversion_constant '_atom_site_anisotrop.U[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[3][3] _item_description.description ; The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[3][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[3][3]_esd' associated_esd '_atom_site.aniso_U[3][3]' conversion_constant '_atom_site_anisotrop.U[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[3][3]. ; _item.name '_atom_site_anisotrop.B[3][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[3][3]' associated_value '_atom_site.aniso_U[3][3]_esd' conversion_constant '_atom_site_anisotrop.U[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.ratio _item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site_anisotrop.ratio' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_ratio' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_related.related_name '_atom_site.aniso_ratio' _item_related.function_code alternate_exclusive _item_type.code float save_ save__atom_site_anisotrop.id _item_description.description ; This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_atom_site_anisotrop.id' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_aniso_label' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site_anisotrop.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_atom_site_anisotrop.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_aniso_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site_anisotrop.U[1][1] _item_description.description ; The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][1]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][1]_esd' associated_esd '_atom_site.aniso_B[1][1]' conversion_constant '_atom_site_anisotrop.B[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][1]. ; _item.name '_atom_site_anisotrop.U[1][1]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][1]' associated_value '_atom_site.aniso_B[1][1]_esd' conversion_constant '_atom_site_anisotrop.B[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][2] _item_description.description ; The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][2]_esd' associated_esd '_atom_site.aniso_B[1][2]' conversion_constant '_atom_site_anisotrop.B[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][2]. ; _item.name '_atom_site_anisotrop.U[1][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][2]' associated_value '_atom_site.aniso_B[1][2]_esd' conversion_constant '_atom_site_anisotrop.B[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][3] _item_description.description ; The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][3]_esd' associated_esd '_atom_site.aniso_B[1][3]' conversion_constant '_atom_site_anisotrop.B[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][3]. ; _item.name '_atom_site_anisotrop.U[1][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][3]' associated_value '_atom_site.aniso_B[1][3]_esd' conversion_constant '_atom_site_anisotrop.B[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][2] _item_description.description ; The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[2][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][2]_esd' associated_esd '_atom_site.aniso_B[2][2]' conversion_constant '_atom_site_anisotrop.B[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[2][2]. ; _item.name '_atom_site_anisotrop.U[2][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][2]' associated_value '_atom_site.aniso_B[2][2]_esd' conversion_constant '_atom_site_anisotrop.B[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][3] _item_description.description ; The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[2][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][3]_esd' associated_esd '_atom_site.aniso_B[2][3]' conversion_constant '_atom_site_anisotrop.B[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[2][3]. ; _item.name '_atom_site_anisotrop.U[2][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][3]' associated_value '_atom_site.aniso_B[2][3]_esd' conversion_constant '_atom_site_anisotrop.B[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[3][3] _item_description.description ; The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[3][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[3][3]_esd' associated_esd '_atom_site.aniso_B[3][3]' conversion_constant '_atom_site_anisotrop.B[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[3][3]. ; _item.name '_atom_site_anisotrop.U[3][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[3][3]' associated_value '_atom_site.aniso_B[3][3]_esd' conversion_constant '_atom_site_anisotrop.B[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive _item_type.code float _item_units.code angstroms_squared save_ ################ ## ATOM_SITES ## ################ save_atom_sites _category.description ; Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. ; _category.id atom_sites _category.mandatory_code no _category_key.name '_atom_sites.entry_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _atom_sites.entry_id '5HVP' _atom_sites.Cartn_transform_axes 'c along z, astar along x, b along y' _atom_sites.Cartn_transf_matrix[1][1] 58.39 _atom_sites.Cartn_transf_matrix[1][2] 0.00 _atom_sites.Cartn_transf_matrix[1][3] 0.00 _atom_sites.Cartn_transf_matrix[2][1] 0.00 _atom_sites.Cartn_transf_matrix[2][2] 86.70 _atom_sites.Cartn_transf_matrix[2][3] 0.00 _atom_sites.Cartn_transf_matrix[3][1] 0.00 _atom_sites.Cartn_transf_matrix[3][2] 0.00 _atom_sites.Cartn_transf_matrix[3][3] 46.27 _atom_sites.Cartn_transf_vector[1] 0.00 _atom_sites.Cartn_transf_vector[2] 0.00 _atom_sites.Cartn_transf_vector[3] 0.00 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_atom_sites.entry_id' _item.mandatory_code yes save_ save__atom_sites.Cartn_transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_vector[1] _item_description.description ; The [1] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transf_vector[2] _item_description.description ; The [2] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transf_vector[3] _item_description.description ; The [3] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transform_axes _item_description.description ; A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites.Cartn_transf_matrix[][]. ; _item.name '_atom_sites.Cartn_transform_axes' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_transform_axes' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'a parallel to x; b in the plane of y and z' save_ save__atom_sites.fract_transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_vector[1] _item_description.description ; The [1] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.fract_transf_vector[2] _item_description.description ; The [2] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.fract_transf_vector[3] _item_description.description ; The [3] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.solution_primary _item_description.description ; This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_primary' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_primary' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ save__atom_sites.solution_secondary _item_description.description ; This code identifies the method used to locate the non-hydrogen-atom sites not found by _atom_sites.solution_primary. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_secondary' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_secondary' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ save__atom_sites.solution_hydrogens _item_description.description ; This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_hydrogens' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_hydrogens' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ #################### ## ATOM_SITES_ALT ## #################### save_atom_sites_alt _category.description ; Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block. ; _category.id atom_sites_alt _category.mandatory_code no _category_key.name '_atom_sites_alt.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_alt.id _atom_sites_alt.details . ; Atom sites with the alternative ID set to null are not modeled in alternative conformations ; 1 ; Atom sites with the alternative ID set to 1 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 2. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 1 correlate with the conformation of the inhibitor marked with alternative ID 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor. ; 2 ; Atom sites with the alternative ID set to 2 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 1. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 2 correlate with the conformation of the inhibitor marked with alternative ID 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor. ; 3 ; Atom sites with the alternative ID set to 3 have been modeled in alternative conformations with respect to atoms marked with alternative ID 4. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; 4 ; Atom sites with the alternative ID set to 4 have been modeled in alternative conformations with respect to atoms marked with alternative ID 3. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt.details _item_description.description ; A description of special aspects of the modelling of atoms in alternative conformations. ; _item.name '_atom_sites_alt.details' _item.category_id atom_sites_alt _item.mandatory_code no _item_type.code text save_ save__atom_sites_alt.id _item_description.description ; The value of _atom_sites_alt.id must uniquely identify a record in the ATOM_SITES_ALT list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt.id' atom_sites_alt yes '_atom_site.label_alt_id' atom_site no '_atom_sites_alt_gen.alt_id' atom_sites_alt_gen yes '_geom_angle.atom_site_label_alt_id_1' geom_angle no '_geom_angle.atom_site_label_alt_id_2' geom_angle no '_geom_angle.atom_site_label_alt_id_3' geom_angle no '_geom_bond.atom_site_label_alt_id_1' geom_bond no '_geom_bond.atom_site_label_alt_id_2' geom_bond no '_geom_contact.atom_site_label_alt_id_1' geom_contact no '_geom_contact.atom_site_label_alt_id_2' geom_contact no '_geom_hbond.atom_site_label_alt_id_A' geom_hbond no '_geom_hbond.atom_site_label_alt_id_D' geom_hbond no '_geom_hbond.atom_site_label_alt_id_H' geom_hbond no '_geom_torsion.atom_site_label_alt_id_1' geom_torsion no '_geom_torsion.atom_site_label_alt_id_2' geom_torsion no '_geom_torsion.atom_site_label_alt_id_3' geom_torsion no '_geom_torsion.atom_site_label_alt_id_4' geom_torsion no '_struct_conn.ptnr1_label_alt_id' struct_conn no '_struct_conn.ptnr2_label_alt_id' struct_conn no '_struct_mon_nucl.label_alt_id' struct_mon_nucl yes '_struct_mon_prot.label_alt_id' struct_mon_prot yes '_struct_mon_prot_cis.label_alt_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_alt_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_alt_id' struct_ncs_dom_lim yes '_struct_site_gen.label_alt_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_alt_id' '_atom_sites_alt.id' '_atom_sites_alt_gen.alt_id' '_atom_sites_alt.id' '_geom_angle.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_angle.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_angle.atom_site_label_alt_id_3' '_atom_site.label_alt_id' '_geom_bond.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_bond.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_contact.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_contact.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_A' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_D' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_H' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_3' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_4' '_atom_site.label_alt_id' '_struct_conn.ptnr1_label_alt_id' '_atom_site.label_alt_id' '_struct_conn.ptnr2_label_alt_id' '_atom_site.label_alt_id' '_struct_mon_nucl.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot_cis.label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_lim.beg_label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_lim.end_label_alt_id' '_atom_site.label_alt_id' '_struct_site_gen.label_alt_id' '_atom_site.label_alt_id' _item_type.code code loop_ _item_examples.case 'orientation 1' 'molecule abc' save_ ######################## ## ATOM_SITES_ALT_ENS ## ######################## save_atom_sites_alt_ens _category.description ; Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs. ; _category.id atom_sites_alt_ens _category.mandatory_code no _category_key.name '_atom_sites_alt_ens.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_alt_ens.id _atom_sites_alt_ens.details 'Ensemble 1-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 1-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt_ens.details _item_description.description ; A description of special aspects of the ensemble structure generated from atoms with various alternative IDs. ; _item.name '_atom_sites_alt_ens.details' _item.category_id atom_sites_alt_ens _item.mandatory_code no _item_type.code text save_ save__atom_sites_alt_ens.id _item_description.description ; The value of _atom_sites_alt_ens.id must uniquely identify a record in the ATOM_SITES_ALT_ENS list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt_ens.id' atom_sites_alt_ens yes '_atom_sites_alt_gen.ens_id' atom_sites_alt_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_ens.id' _item_type.code code save_ ######################## ## ATOM_SITES_ALT_GEN ## ######################## save_atom_sites_alt_gen _category.description ; Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. ; _category.id atom_sites_alt_gen _category.mandatory_code no loop_ _category_key.name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_gen.alt_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_alt_gen.ens_id _atom_sites_alt_gen.alt_id 'Ensemble 1-A' . 'Ensemble 1-A' 1 'Ensemble 1-A' 3 'Ensemble 1-B' . 'Ensemble 1-B' 1 'Ensemble 1-B' 4 'Ensemble 2-A' . 'Ensemble 2-A' 2 'Ensemble 2-A' 3 'Ensemble 2-B' . 'Ensemble 2-B' 2 'Ensemble 2-B' 4 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt_gen.alt_id _item_description.description ; This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_atom_sites_alt_gen.alt_id' _item.mandatory_code yes save_ save__atom_sites_alt_gen.ens_id _item_description.description ; This data item is a pointer to _atom_sites_alt_ens.id in the ATOM_SITES_ALT_ENS category. ; _item.name '_atom_sites_alt_gen.ens_id' _item.mandatory_code yes save_ ######################### ## ATOM_SITES_FOOTNOTE ## ######################### save_atom_sites_footnote _category.description ; Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites. ; _category.id atom_sites_footnote _category.mandatory_code no _category_key.name '_atom_sites_footnote.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_footnote.id _atom_sites_footnote.text 1 ; The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative IDs *1* and *2*. ; 2 ; Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 3 ; The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 4 ; Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor. ; 5 ; The positions of these water molecules correlate with alternative orientations of amino-acid side chains that do not correlate with alternative orientations of the inhibitor. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_footnote.id _item_description.description ; A code that identifies the footnote. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_footnote.id' atom_sites_footnote yes '_atom_site.footnote_id' atom_site no loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.footnote_id' '_atom_sites_footnote.id' _item_type.code code loop_ _item_examples.case 'a' 'b' '1' '2' save_ save__atom_sites_footnote.text _item_description.description ; The text of the footnote. Footnotes are used to describe an atom site or a group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modelled. ; _item.name '_atom_sites_footnote.text' _item.category_id atom_sites_footnote _item.mandatory_code no _item_type.code text save_ ############### ## ATOM_TYPE ## ############### save_atom_type _category.description ; Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors. ; _category.id atom_type _category.mandatory_code no _category_key.name '_atom_type.symbol' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c C 0 2.31000 20.8439 1.02000 10.2075 1.58860 0.568700 0.865000 51.6512 0.21560 N 0 12.2126 0.005700 3.13220 9.89330 2.01250 28.9975 1.16630 0.582600 -11.529 O 0 3.04850 13.2771 2.28680 5.70110 1.54630 0.323900 0.867000 32.9089 0.250800 S 0 6.90530 1.46790 5.20340 22.2151 1.43790 0.253600 1.58630 56.1720 0.866900 CL -1 18.2915 0.006600 7.20840 1.17170 6.53370 19.5424 2.33860 60.4486 -16.378 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.number_in_cell _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_source C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_type.analytical_mass_percent _item_description.description ; Mass percentage of this atom type derived from chemical analysis. ; _item.name '_atom_type.analytical_mass_percent' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_analytical_mass_%' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__atom_type.description _item_description.description ; A description of the atom(s) designated by this atom type. In most cases, this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. ; _item.name '_atom_type.description' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'deuterium' '0.34Fe+0.66Ni' save_ save__atom_type.number_in_cell _item_description.description ; Total number of atoms of this atom type in the unit cell. ; _item.name '_atom_type.number_in_cell' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_number_in_cell' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__atom_type.oxidation_number _item_description.description ; Formal oxidation state of this atom type in the structure. ; _item.name '_atom_type.oxidation_number' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_oxidation_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 -8 -8 -8 _item_type.code int save_ save__atom_type.radius_bond _item_description.description ; The effective intramolecular bonding radius in angstroms of this atom type. ; _item.name '_atom_type.radius_bond' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_bond' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 5.0 5.0 5.0 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__atom_type.radius_contact _item_description.description ; The effective intermolecular bonding radius in angstroms of this atom type. ; _item.name '_atom_type.radius_contact' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_contact' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 5.0 5.0 5.0 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__atom_type.scat_Cromer_Mann_a1 _item_description.description ; The Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a1' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a2 _item_description.description ; The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a2' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a3 _item_description.description ; The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a3' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a4 _item_description.description ; The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a4' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b1 _item_description.description ; The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b1' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b2 _item_description.description ; The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b2' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b3 _item_description.description ; The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b3' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b4 _item_description.description ; The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b4' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_c _item_description.description ; The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_c' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_c' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' _item_type.code float save_ save__atom_type.scat_dispersion_imag _item_description.description ; The imaginary component of the anomalous-dispersion scattering factor, f'', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id. ; _item.name '_atom_type.scat_dispersion_imag' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_imag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_real' _item_type.code float save_ save__atom_type.scat_dispersion_real _item_description.description ; The real component of the anomalous-dispersion scattering factor, f', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id. ; _item.name '_atom_type.scat_dispersion_real' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_real' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_imag' _item_type.code float save_ save__atom_type.scat_length_neutron _item_description.description ; The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. ; _item.name '_atom_type.scat_length_neutron' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_length_neutron' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_units.code femtometres save_ save__atom_type.scat_source _item_description.description ; Reference to the source of the scattering factors or scattering lengths used for this atom type. ; _item.name '_atom_type.scat_source' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_source' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'International Tables Vol. IV Table 2.4.6B' save_ save__atom_type.scat_versus_stol_list _item_description.description ; A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. ; _item.name '_atom_type.scat_versus_stol_list' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_versus_stol_list' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__atom_type.symbol _item_description.description ; The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_type.symbol' atom_type yes '_atom_site.type_symbol' atom_site yes '_atom_site_anisotrop.type_symbol' atom_site_anisotrop yes '_chemical_conn_atom.type_symbol' chemical_conn_atom yes '_chem_comp_atom.type_symbol' chem_comp_atom yes '_phasing_MIR_der_site.atom_type_symbol' phasing_MIR_der_site yes _item_aliases.alias_name '_atom_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.type_symbol' '_atom_type.symbol' '_atom_site_anisotrop.type_symbol' '_atom_type.symbol' '_chemical_conn_atom.type_symbol' '_atom_type.symbol' '_chem_comp_atom.type_symbol' '_atom_type.symbol' '_phasing_MIR_der_site.atom_type_symbol' '_atom_type.symbol' _item_type.code code loop_ _item_examples.case 'C' 'Cu2+' 'H(SDS)' 'dummy' 'FeNi' save_ ########### ## AUDIT ## ########### save_audit _category.description ; Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block. ; _category.id audit _category.mandatory_code no _category_key.name '_audit.revision_id' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _audit.revision_id 1 _audit.creation_date '1992-12-08' _audit.creation_method ; Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records ; _audit.update_record ; 1992-12-09 adjusted to reflect comments from B. McKeever 1992-12-10 adjusted to reflect comments from H. Berman 1992-12-12 adjusted to reflect comments from K. Watenpaugh ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _audit.creation_date 1991-03-20 _audit.creation_method from_xtal_archive_file_using_CIFIO _audit.update_record ; 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec'd by co-editor as manuscript HL0007. 1991-04-17 adjustments based on first referee report. 1991-04-18 adjustments based on second referee report. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit.creation_date _item_description.description ; A date that the data block was created. The date format is yyyy-mm-dd. ; _item.name '_audit.creation_date' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_creation_date' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd _item_examples.case '1990-07-12' save_ save__audit.creation_method _item_description.description ; A description of how data were entered into the data block. ; _item.name '_audit.creation_method' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_creation_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'spawned by the program QBEE' save_ save__audit.revision_id _item_description.description ; The value of _audit.revision_id must uniquely identify a record in the AUDIT list. ; _item.name '_audit.revision_id' _item.category_id audit _item.mandatory_code yes _item_type.code code _item_examples.case 'rev1' save_ save__audit.update_record _item_description.description ; A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. ; _item.name '_audit.update_record' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_update_record' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '1990-07-15 Updated by the Co-editor' save_ ################## ## AUDIT_AUTHOR ## ################## save_audit_author _category.description ; Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. ; _category.id audit_author _category.mandatory_code no _category_key.name '_audit_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _audit_author.name _audit_author.address 'Fitzgerald, Paula M.D.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'McKeever, Brian M.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Van Middlesworth, J.F.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Springer, James P.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_author.address _item_description.description ; The address of an author of this data block. If there are multiple authors, _audit_author.address is looped with _audit_author.name. ; _item.name '_audit_author.address' _item.category_id audit_author _item.mandatory_code no _item_aliases.alias_name '_audit_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__audit_author.name _item_description.description ; The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_audit_author.name' _item.category_id audit_author _item.mandatory_code yes _item_aliases.alias_name '_audit_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ ################### ## AUDIT_CONFORM ## ################### save_audit_conform _category.description ; Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. ; _category.id audit_conform _category.mandatory_code no loop_ _category_key.name '_audit_conform.dict_name' '_audit_conform.dict_version' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - any file conforming to the current CIF core dictionary. ; ; _audit_conform.dict_name cif_core.dic _audit_conform.dict_version 2.3.1 _audit_conform.dict_location ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_conform.dict_location _item_description.description ; A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. ; _item.name '_audit_conform.dict_location' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_location' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__audit_conform.dict_name _item_description.description ; The string identifying the highest-level dictionary defining data names used in this file. ; _item.name '_audit_conform.dict_name' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__audit_conform.dict_version _item_description.description ; The version number of the dictionary to which the current data block conforms. ; _item.name '_audit_conform.dict_version' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_version' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ########################## ## AUDIT_CONTACT_AUTHOR ## ########################## save_audit_contact_author _category.description ; Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block. ; _category.id audit_contact_author _category.mandatory_code no _category_key.name '_audit_contact_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _audit_contact_author.name 'Fitzgerald, Paula M.D.' _audit_contact_author.address ; Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; _audit_contact_author.phone '1(908)5945510' _audit_contact_author.fax '1(908)5946645' _audit_contact_author.email 'paula_fitzgerald@merck.com' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_contact_author.address _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed. ; _item.name '_audit_contact_author.address' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__audit_contact_author.email _item_description.description ; The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; _item.name '_audit_contact_author.email' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'name@host.domain.country' 'bm@iucr.org' save_ save__audit_contact_author.fax _item_description.description ; The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. ; _item.name '_audit_contact_author.fax' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477334' '12()349477334' save_ save__audit_contact_author.name _item_description.description ; The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_audit_contact_author.name' _item.category_id audit_contact_author _item.mandatory_code yes _item_aliases.alias_name '_audit_contact_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__audit_contact_author.phone _item_description.description ; The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. ; _item.name '_audit_contact_author.phone' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477330' '12()349477330' '12(34)9477330x5543' save_ ########## ## CELL ## ########## save_cell _category.description ; Data items in the CELL category record details about the crystallographic cell parameters. ; _category.id cell _category.mandatory_code no _category_key.name '_cell.entry_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _cell.entry_id '5HVP' _cell.length_a 58.39 _cell.length_a_esd 0.05 _cell.length_b 86.70 _cell.length_b_esd 0.12 _cell.length_c 46.27 _cell.length_c_esd 0.06 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.volume 234237 _cell.details ; The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _cell.length_a 5.959 _cell.length_a_esd 0.001 _cell.length_b 14.956 _cell.length_b_esd 0.001 _cell.length_c 19.737 _cell.length_c_esd 0.003 _cell.angle_alpha 90.0 _cell.angle_beta 90.0 _cell.angle_gamma 90.0 _cell.volume 1759.0 _cell.volume_esd 0.3 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell.angle_alpha _item_description.description ; Unit-cell angle alpha of the reported structure in degrees. ; _item.name '_cell.angle_alpha' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_alpha' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_beta' '_cell.angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_alpha_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_alpha_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.angle_alpha. ; _item.name '_cell.angle_alpha_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_beta_esd' '_cell.angle_gamma_esd' _item_related.related_name '_cell.angle_alpha' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.angle_beta _item_description.description ; Unit-cell angle beta of the reported structure in degrees. ; _item.name '_cell.angle_beta' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_beta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_beta_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_beta_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.angle_beta. ; _item.name '_cell.angle_beta_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_gamma_esd' _item_related.related_name '_cell.angle_beta' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.angle_gamma _item_description.description ; Unit-cell angle gamma of the reported structure in degrees. ; _item.name '_cell.angle_gamma' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_gamma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_beta' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_gamma_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_gamma_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.angle_gamma. ; _item.name '_cell.angle_gamma_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_beta_esd' _item_related.related_name '_cell.angle_gamma' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_cell.entry_id' _item.mandatory_code yes save_ save__cell.details _item_description.description ; A description of special aspects of the cell choice, noting possible alternative settings. ; _item.name '_cell.details' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'pseudo-orthorhombic' 'standard setting from 45 deg rotation around c' save_ save__cell.formula_units_Z _item_description.description ; The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum. ; _item.name '_cell.formula_units_Z' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_formula_units_Z' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__cell.length_a _item_description.description ; Unit-cell length a corresponding to the structure reported in angstroms. ; _item.name '_cell.length_a' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_a' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_a_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_a_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.length_a. ; _item.name '_cell.length_a_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_b_esd' '_cell.length_c_esd' _item_related.related_name '_cell.length_a' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.length_b _item_description.description ; Unit-cell length b corresponding to the structure reported in angstroms. ; _item.name '_cell.length_b' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_b' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell.length_a' '_cell.length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_b_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_b_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.length_b. ; _item.name '_cell.length_b_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_c_esd' _item_related.related_name '_cell.length_b' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.length_c _item_description.description ; Unit-cell length c corresponding to the structure reported in angstroms. ; _item.name '_cell.length_c' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_c' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell.length_a' '_cell.length_b' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_c_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_c_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.length_c. ; _item.name '_cell.length_c_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_b_esd' _item_related.related_name '_cell.length_c' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.volume _item_description.description ; Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = _cell.length_a b = _cell.length_b c = _cell.length_c alpha = _cell.angle_alpha beta = _cell.angle_beta gamma = _cell.angle_gamma ; _item.name '_cell.volume' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_volume' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.volume_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__cell.volume_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.volume. ; _item.name '_cell.volume_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_cell.volume' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ save__cell.Z_PDB _item_description.description ; The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; _item.name '_cell.Z_PDB' _item.category_id cell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ ###################### ## CELL_MEASUREMENT ## ###################### save_cell_measurement _category.description ; Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. ; _category.id cell_measurement _category.mandatory_code no _category_key.name '_cell_measurement.entry_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _cell_measurement.entry_id '5HVP' _cell_measurement.temp 293 _cell_measurement.temp_esd 3 _cell_measurement.theta_min 11 _cell_measurement.theta_max 31 _cell_measurement.wavelength 1.54 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _cell_measurement.temp 293 _cell_measurement.reflns_used 25 _cell_measurement.theta_min 25 _cell_measurement.theta_max 31 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell_measurement.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_cell_measurement.entry_id' _item.mandatory_code yes save_ save__cell_measurement.pressure _item_description.description ; The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized). ; _item.name '_cell_measurement.pressure' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_pressure' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_cell_measurement.pressure_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kilopascals save_ save__cell_measurement.pressure_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell_measurement.pressure. ; _item.name '_cell_measurement.pressure_esd' _item.category_id cell_measurement _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_cell_measurement.pressure' _item_related.function_code associated_value _item_type.code float _item_units.code kilopascals save_ save__cell_measurement.radiation _item_description.description ; Description of the radiation used to measure the unit-cell data. See also _cell_measurement.wavelength. ; _item.name '_cell_measurement.radiation' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_radiation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'neutron' 'Cu K\a' 'synchrotron' save_ save__cell_measurement.reflns_used _item_description.description ; The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. ; _item.name '_cell_measurement.reflns_used' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_reflns_used' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__cell_measurement.temp _item_description.description ; The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). ; _item.name '_cell_measurement.temp' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_temperature' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell_measurement.temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvins save_ save__cell_measurement.temp_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell_measurement.temp. ; _item.name '_cell_measurement.temp_esd' _item.category_id cell_measurement _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_cell_measurement.temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvins save_ save__cell_measurement.theta_max _item_description.description ; The maximum theta angle of reflections used to measure the unit cell in degrees. ; _item.name '_cell_measurement.theta_max' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__cell_measurement.theta_min _item_description.description ; The minimum theta angle of reflections used to measure the unit cell in degrees. ; _item.name '_cell_measurement.theta_min' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__cell_measurement.wavelength _item_description.description ; The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be that specified in the category DIFFRN_RADIATION_WAVELENGTH. ; _item.name '_cell_measurement.wavelength' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ ############################ ## CELL_MEASUREMENT_REFLN ## ############################ save_cell_measurement_refln _category.description ; Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. ; _category.id cell_measurement_refln _category.mandatory_code no loop_ _category_key.name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room temperature (unpublished). ; ; loop_ _cell_measurement_refln.index_h _cell_measurement_refln.index_k _cell_measurement_refln.index_l _cell_measurement_refln.theta -2 4 1 8.67 0 3 2 9.45 3 0 2 9.46 -3 4 1 8.93 -2 1 -2 7.53 10 0 0 23.77 0 10 0 23.78 -5 4 1 11.14 # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell_measurement_refln.index_h _item_description.description ; Miller index h of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_h' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.index_k _item_description.description ; Miller index k of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_k' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.index_l _item_description.description ; Miller index l of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_l' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.theta _item_description.description ; Theta angle for a reflection used for measurement of the unit cell in degrees. ; _item.name '_cell_measurement_refln.theta' _item.category_id cell_measurement_refln _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_refln_theta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ ############### ## CHEM_COMP ## ############### save_chem_comp _category.description ; Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components. ; _category.id chem_comp _category.mandatory_code no _category_key.name '_chem_comp.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp.id _chem_comp.model_source _chem_comp.name phe '1987 Protin/Prolsq Ideals file' phenylalanine val '1987 Protin/Prolsq Ideals file' alanine # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp.formula _item_description.description ; The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. ; _item.name '_chem_comp.formula' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'C18 H19 N7 O8 S' save_ save__chem_comp.formula_weight _item_description.description ; Formula mass in daltons of the chemical component. ; _item.name '_chem_comp.formula_weight' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__chem_comp.id _item_description.description ; The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.id' chem_comp yes '_atom_site.label_comp_id' atom_site no '_chem_comp.mon_nstd_parent_comp_id' chem_comp no '_chem_comp_atom.comp_id' chem_comp_atom yes '_chem_comp_angle.comp_id' chem_comp_angle yes '_chem_comp_bond.comp_id' chem_comp_bond yes '_chem_comp_chir.comp_id' chem_comp_chir yes '_chem_comp_chir_atom.comp_id' chem_comp_chir_atom yes '_chem_comp_plane.comp_id' chem_comp_plane yes '_chem_comp_plane_atom.comp_id' chem_comp_plane_atom yes '_chem_comp_tor.comp_id' chem_comp_tor yes '_chem_comp_tor_value.comp_id' chem_comp_tor_value yes '_entity_poly_seq.mon_id' entity_poly_seq yes '_geom_angle.atom_site_label_comp_id_1' geom_angle no '_geom_angle.atom_site_label_comp_id_2' geom_angle no '_geom_angle.atom_site_label_comp_id_3' geom_angle no '_geom_bond.atom_site_label_comp_id_1' geom_bond no '_geom_bond.atom_site_label_comp_id_2' geom_bond no '_geom_contact.atom_site_label_comp_id_1' geom_contact no '_geom_contact.atom_site_label_comp_id_2' geom_contact no '_geom_hbond.atom_site_label_comp_id_A' geom_hbond no '_geom_hbond.atom_site_label_comp_id_D' geom_hbond no '_geom_hbond.atom_site_label_comp_id_H' geom_hbond no '_geom_torsion.atom_site_label_comp_id_1' geom_torsion no '_geom_torsion.atom_site_label_comp_id_2' geom_torsion no '_geom_torsion.atom_site_label_comp_id_3' geom_torsion no '_geom_torsion.atom_site_label_comp_id_4' geom_torsion no '_struct_conf.beg_label_comp_id' struct_conf yes '_struct_conf.end_label_comp_id' struct_conf yes '_struct_conn.ptnr1_label_comp_id' struct_conn yes '_struct_conn.ptnr2_label_comp_id' struct_conn yes '_struct_mon_nucl.label_comp_id' struct_mon_nucl yes '_struct_mon_prot.label_comp_id' struct_mon_prot yes '_struct_mon_prot_cis.label_comp_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_comp_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_comp_id' struct_ncs_dom_lim yes '_struct_ref_seq_dif.db_mon_id' struct_ref_seq_dif yes '_struct_ref_seq_dif.mon_id' struct_ref_seq_dif yes '_struct_sheet_range.beg_label_comp_id' struct_sheet_range yes '_struct_sheet_range.end_label_comp_id' struct_sheet_range yes '_struct_site_gen.label_comp_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_comp_id' '_chem_comp.id' '_chem_comp.mon_nstd_parent_comp_id' '_chem_comp.id' '_chem_comp_atom.comp_id' '_chem_comp.id' '_chem_comp_chir.comp_id' '_chem_comp.id' '_chem_comp_chir_atom.comp_id' '_chem_comp.id' '_chem_comp_plane.comp_id' '_chem_comp.id' '_chem_comp_plane_atom.comp_id' '_chem_comp.id' '_entity_poly_seq.mon_id' '_chem_comp.id' '_chem_comp_angle.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_bond.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_tor.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_tor_value.comp_id' '_chem_comp_atom.comp_id' '_geom_angle.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_angle.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_angle.atom_site_label_comp_id_3' '_atom_site.label_comp_id' '_geom_bond.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_bond.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_contact.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_contact.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_A' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_D' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_H' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_3' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_4' '_atom_site.label_comp_id' '_struct_conf.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_conf.end_label_comp_id' '_atom_site.label_comp_id' '_struct_conn.ptnr1_label_comp_id' '_atom_site.label_comp_id' '_struct_conn.ptnr2_label_comp_id' '_atom_site.label_comp_id' '_struct_mon_nucl.label_comp_id' '_atom_site.label_comp_id' '_struct_mon_prot.label_comp_id' '_atom_site.label_comp_id' '_struct_mon_prot_cis.label_comp_id' '_atom_site.label_comp_id' '_struct_ncs_dom_lim.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_ncs_dom_lim.end_label_comp_id' '_atom_site.label_comp_id' '_struct_ref_seq_dif.db_mon_id' '_chem_comp.id' '_struct_ref_seq_dif.mon_id' '_chem_comp.id' '_struct_sheet_range.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_sheet_range.end_label_comp_id' '_atom_site.label_comp_id' '_struct_site_gen.label_comp_id' '_atom_site.label_comp_id' _item_type.code ucode loop_ _item_examples.case 'ala' 'val' 'A' 'C' save_ save__chem_comp.model_details _item_description.description ; A description of special aspects of the generation of the coordinates for the model of the component. ; _item.name '_chem_comp.model_details' _item.category_id chem_comp _item.mandatory_code no _item_type.code text _item_examples.case 'geometry idealized but not minimized' save_ save__chem_comp.model_erf _item_description.description ; A pointer to an external reference file from which the atomic description of the component is taken. ; _item.name '_chem_comp.model_erf' _item.category_id chem_comp _item.mandatory_code no _item_type.code line save_ save__chem_comp.model_source _item_description.description ; The source of the coordinates for the model of the component. ; _item.name '_chem_comp.model_source' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CSD entry ABCDEF' 'built using Quanta/Charmm' save_ save__chem_comp.mon_nstd_class _item_description.description ; A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer. ; _item.name '_chem_comp.mon_nstd_class' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'iodinated base' 'phosphorylated amino acid' 'brominated base' 'modified amino acid' 'glycosylated amino acid' save_ save__chem_comp.mon_nstd_details _item_description.description ; A description of special details of a nonstandard monomer. ; _item.name '_chem_comp.mon_nstd_details' _item.category_id chem_comp _item.mandatory_code no _item_type.code text save_ save__chem_comp.mon_nstd_flag _item_description.description ; 'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and _chem_comp.mon_nstd_details data items. ; _item.name '_chem_comp.mon_nstd_flag' _item.category_id chem_comp _item.mandatory_code no _item_type.code ucode _item_default.value no loop_ _item_enumeration.value _item_enumeration.detail no 'the monomer is nonstandard' n 'abbreviation for "no"' yes 'the monomer is standard' y 'abbreviation for "yes"' save_ save__chem_comp.mon_nstd_parent _item_description.description ; The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer. ; _item.name '_chem_comp.mon_nstd_parent' _item.category_id chem_comp _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'tyrosine' 'cytosine' save_ save__chem_comp.mon_nstd_parent_comp_id _item_description.description ; The identifier for the parent component of the nonstandard component. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp.mon_nstd_parent_comp_id' _item.mandatory_code no save_ save__chem_comp.name _item_description.description ; The full name of the component. ; _item.name '_chem_comp.name' _item.category_id chem_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'alanine' 'valine' 'adenine' 'cytosine' save_ save__chem_comp.number_atoms_all _item_description.description ; The total number of atoms in the component. ; _item.name '_chem_comp.number_atoms_all' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__chem_comp.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the component. ; _item.name '_chem_comp.number_atoms_nh' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__chem_comp.one_letter_code _item_description.description ; For standard polymer components, the one-letter code for the component. If there is not a standard one-letter code for this component, or if this is a non-polymer component, the one-letter code should be given as 'X'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. ; _item.name '_chem_comp.one_letter_code' _item.category_id chem_comp _item.mandatory_code no _item_type.code uchar1 loop_ _item_examples.case _item_examples.detail A 'alanine or adenine' B 'ambiguous asparagine/aspartic acid' R 'arginine' N 'asparagine' D 'aspartic acid' C 'cysteine or cystine or cytosine' Q 'glutamine' E 'glutamic acid' Z 'ambiguous glutamine/glutamic acid' G 'glycine or guanine' H 'histidine' I 'isoleucine' L 'leucine' K 'lysine' M 'methionine' F 'phenylalanine' P 'proline' S 'serine' T 'threonine or thymine' W 'tryptophan' Y 'tyrosine' V 'valine' U 'uracil' O 'water' X 'other' save_ save__chem_comp.three_letter_code _item_description.description ; For standard polymer components, the three-letter code for the component. If there is not a standard three-letter code for this component, or if this is a non-polymer component, the three-letter code should be given as 'UNK'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. ; _item.name '_chem_comp.three_letter_code' _item.category_id chem_comp _item.mandatory_code no _item_type.code uchar3 loop_ _item_examples.case _item_examples.detail ALA 'alanine' ARG 'arginine' ASN 'asparagine' ASP 'aspartic acid' ASX 'ambiguous asparagine/aspartic acid' CYS 'cysteine' GLN 'glutamine' GLU 'glutamic acid' GLY 'glycine' GLX 'ambiguous glutamine/glutamic acid' HIS 'histidine' ILE 'isoleucine' LEU 'leucine' LYS 'lysine' MET 'methionine' PHE 'phenylalanine' PRO 'proline' SER 'serine' THR 'threonine' TRP 'tryptophan' TRY 'tyrosine' VAL 'valine' 1MA '1-methyladenosine' 5MC '5-methylcytosine' OMC '2(prime)-O-methylcytodine' 1MG '1-methylguanosine' 2MG 'N(2)-methylguanosine' M2G 'N(2)-dimethylguanosine' 7MG '7-methylguanosine' 0MG '2(prime)-O-methylguanosine' H2U 'dihydrouridine' 5MU 'ribosylthymidine' PSU 'pseudouridine' ACE 'acetic acid' FOR 'formic acid' HOH 'water' UNK 'other' save_ save__chem_comp.type _item_description.description ; For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.type' chem_comp yes '_chem_comp_link.type_comp_1' chem_comp_link yes '_chem_comp_link.type_comp_2' chem_comp_link yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_link.type_comp_1' '_chem_comp.type' '_chem_comp_link.type_comp_2' '_chem_comp.type' _item_type.code uline loop_ _item_enumeration.value 'D-peptide linking' 'L-peptide linking' 'D-peptide NH3 amino terminus' 'L-peptide NH3 amino terminus' 'D-peptide COOH carboxy terminus' 'L-peptide COOH carboxy terminus' 'DNA linking' 'RNA linking' 'DNA OH 5 prime terminus' 'RNA OH 5 prime terminus' 'DNA OH 3 prime terminus' 'RNA OH 3 prime terminus' 'D-saccharide 1,4 and 1,4 linking' 'L-saccharide 1,4 and 1,4 linking' 'D-saccharide 1,4 and 1,6 linking' 'L-saccharide 1,4 and 1,6 linking' 'L-saccharide' 'D-saccharide' 'saccharide' 'non-polymer' 'other' save_ ##################### ## CHEM_COMP_ANGLE ## ##################### save_chem_comp_angle _category.description ; Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. ; _category.id chem_comp_angle _category.mandatory_code no loop_ _category_key.name '_chem_comp_angle.comp_id' '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_2' '_chem_comp_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_dist phe N CA C xxx.xx x.xx phe CA C O xxx.xx x.xx phe CB CA C xxx.xx x.xx phe CB CA N xxx.xx x.xx phe CA CB CG xxx.xx x.xx phe CB CG CD1 xxx.xx x.xx phe CB CG CD2 xxx.xx x.xx phe CD1 CG CD2 xxx.xx x.xx phe CG CD1 CE1 xxx.xx x.xx phe CD1 CE1 CZ xxx.xx x.xx phe CE1 CZ CE2 xxx.xx x.xx phe CZ CE2 CD2 xxx.xx x.xx phe CG CD2 CE2 xxx.xx x.xx val N CA C xxx.xx x.xx val CA C O xxx.xx x.xx val CB CA C xxx.xx x.xx val CB CA N xxx.xx x.xx val CA CB CG1 xxx.xx x.xx val CA CB CG2 xxx.xx x.xx val CG1 CB CG2 xxx.xx x.xx ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_angle.atom_id_1 _item_description.description ; The ID of the first of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_angle.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_2' '_chem_comp_angle.atom_id_3' save_ save__chem_comp_angle.atom_id_2 _item_description.description ; The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_angle.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_3' save_ save__chem_comp_angle.atom_id_3 _item_description.description ; The ID of the third of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_angle.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_2' save_ save__chem_comp_angle.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_angle.comp_id' _item.mandatory_code yes save_ save__chem_comp_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_comp_angle.value_angle' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_comp_angle.value_angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_angle. ; _item.name '_chem_comp_angle.value_angle_esd' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_comp_angle.value_dist _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_chem_comp_angle.value_dist' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_angle.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_dist. ; _item.name '_chem_comp_angle.value_dist_esd' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_ATOM ## #################### save_chem_comp_atom _category.description ; Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories. ; _category.id chem_comp_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_atom.comp_id' '_chem_comp_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.substruct_code _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z phe N N main 1.20134 0.84658 0.00000 phe CA C main 0.00000 0.00000 0.00000 phe C C main -1.25029 0.88107 0.00000 phe O O main -2.18525 0.66029 -0.78409 phe CB C side 0.00662 -1.03603 1.11081 phe CG C side 0.03254 -0.49711 2.50951 phe CD1 C side -1.15813 -0.12084 3.13467 phe CE1 C side -1.15720 0.38038 4.42732 phe CZ C side 0.05385 0.51332 5.11032 phe CE2 C side 1.26137 0.11613 4.50975 phe CD2 C side 1.23668 -0.38351 3.20288 val N N main 1.20134 0.84658 0.00000 val CA C main 0.00000 0.00000 0.00000 val C C main -1.25029 0.88107 0.00000 val O O main -2.18525 0.66029 -0.78409 val CB C side 0.05260 -0.99339 1.17429 val CG1 C side -0.13288 -0.31545 2.52668 val CG2 C side -0.94265 -2.12930 0.99811 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_atom.alt_atom_id _item_description.description ; An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. ; _item.name '_chem_comp_atom.alt_atom_id' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code line save_ save__chem_comp_atom.atom_id _item_description.description ; The value of _chem_comp_atom.atom_id must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_atom.atom_id' chem_comp_atom yes '_atom_site.label_atom_id' atom_site no '_chem_comp_angle.atom_id_1' chem_comp_angle yes '_chem_comp_angle.atom_id_2' chem_comp_angle yes '_chem_comp_angle.atom_id_3' chem_comp_angle yes '_chem_comp_bond.atom_id_1' chem_comp_bond yes '_chem_comp_bond.atom_id_2' chem_comp_bond yes '_chem_comp_chir.atom_id' chem_comp_chir yes '_chem_comp_chir_atom.atom_id' chem_comp_chir_atom yes '_chem_comp_plane_atom.atom_id' chem_comp_plane_atom yes '_chem_comp_tor.atom_id_1' chem_comp_tor yes '_chem_comp_tor.atom_id_2' chem_comp_tor yes '_chem_comp_tor.atom_id_3' chem_comp_tor yes '_chem_comp_tor.atom_id_4' chem_comp_tor yes '_geom_angle.atom_site_label_atom_id_1' geom_angle no '_geom_angle.atom_site_label_atom_id_2' geom_angle no '_geom_angle.atom_site_label_atom_id_3' geom_angle no '_geom_bond.atom_site_label_atom_id_1' geom_bond no '_geom_bond.atom_site_label_atom_id_2' geom_bond no '_geom_contact.atom_site_label_atom_id_1' geom_contact no '_geom_contact.atom_site_label_atom_id_2' geom_contact no '_geom_hbond.atom_site_label_atom_id_A' geom_hbond no '_geom_hbond.atom_site_label_atom_id_D' geom_hbond no '_geom_hbond.atom_site_label_atom_id_H' geom_hbond no '_geom_torsion.atom_site_label_atom_id_1' geom_torsion no '_geom_torsion.atom_site_label_atom_id_2' geom_torsion no '_geom_torsion.atom_site_label_atom_id_3' geom_torsion no '_geom_torsion.atom_site_label_atom_id_4' geom_torsion no '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_sheet_hbond.range_1_beg_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_1_end_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_beg_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_end_label_atom_id' struct_sheet_hbond yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_3' '_chem_comp_atom.atom_id' '_chem_comp_bond.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_bond.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_chir.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_chir_atom.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_plane_atom.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_3' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_4' '_chem_comp_atom.atom_id' '_geom_angle.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_angle.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_angle.atom_site_label_atom_id_3' '_atom_site.label_atom_id' '_geom_bond.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_bond.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_contact.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_contact.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_A' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_D' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_H' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_3' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_4' '_atom_site.label_atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_1_beg_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_1_end_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_2_beg_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_2_end_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code atcode save_ save__chem_comp_atom.charge _item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chem_comp_atom.charge' _item.category_id chem_comp_atom _item.mandatory_code no _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 -8 -8 -8 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' save_ save__chem_comp_atom.model_Cartn_x _item_description.description ; The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. ; _item.name '_chem_comp_atom.model_Cartn_x' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_y' '_chem_comp_atom.model_Cartn_z' _item_related.related_name '_chem_comp_atom.model_Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_x. ; _item.name '_chem_comp_atom.model_Cartn_x_esd' _item.category_id chem_comp_atom _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_y_esd' '_chem_comp_atom.model_Cartn_z_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_y _item_description.description ; The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. ; _item.name '_chem_comp_atom.model_Cartn_y' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x' '_chem_comp_atom.model_Cartn_z' _item_related.related_name '_chem_comp_atom.model_Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_y. ; _item.name '_chem_comp_atom.model_Cartn_y_esd' _item.category_id chem_comp_atom _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x_esd' '_chem_comp_atom.model_Cartn_z_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_z _item_description.description ; The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. ; _item.name '_chem_comp_atom.model_Cartn_z' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x' '_chem_comp_atom.model_Cartn_y' _item_related.related_name '_chem_comp_atom.model_Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_z. ; _item.name '_chem_comp_atom.model_Cartn_z_esd' _item.category_id chem_comp_atom _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x_esd' '_chem_comp_atom.model_Cartn_y_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_atom.partial_charge _item_description.description ; The partial charge assigned to this atom. ; _item.name '_chem_comp_atom.partial_charge' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code float save_ save__chem_comp_atom.substruct_code _item_description.description ; This data item assigns the atom to a substructure of the component, if appropriate. ; _item.name '_chem_comp_atom.substruct_code' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail main 'main chain of an amino acid' side 'side chain of an amino acid' base 'base of a nucleic acid' phos 'phosphate of a nucleic acid' sugar 'sugar of a nucleic acid' none 'not appropriate for this monomer' save_ #save_chem_comp_atom.type_energy # _item_description.description #; This data item is a pointer to _atom_type_energy.type in the # ATOM_TYPE_ENERGY category. #; # save_ save__chem_comp_atom.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_chem_comp_atom.type_symbol' _item.mandatory_code yes save_ #################### ## CHEM_COMP_BOND ## #################### save_chem_comp_bond _category.description ; Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both. ; _category.id chem_comp_bond _category.mandatory_code no loop_ _category_key.name '_chem_comp_bond.comp_id' '_chem_comp_bond.atom_id_1' '_chem_comp_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order phe N CA sing phe CA C sing phe C O doub phe CB CA sing phe CB CG sing phe CG CD1 arom phe CD1 CE1 arom phe CE1 CZ arom phe CZ CE2 arom phe CE2 CD2 arom phe CD2 CG arom val N CA sing val CA C sing val C O doub val CB CA sing val CB CG1 sing val CB CG2 sing ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_bond.atom_id_1 _item_description.description ; The ID of the first of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_bond.atom_id_1' _item.mandatory_code yes _item_dependent.dependent_name '_chem_comp_bond.atom_id_2' save_ save__chem_comp_bond.atom_id_2 _item_description.description ; The ID of the second of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_bond.atom_id_2' _item.mandatory_code yes _item_dependent.dependent_name '_chem_comp_bond.atom_id_1' save_ save__chem_comp_bond.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_bond.comp_id' _item.mandatory_code yes save_ save__chem_comp_bond.value_order _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_chem_comp_bond.value_order' _item.category_id chem_comp_bond _item.mandatory_code no _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' save_ save__chem_comp_bond.value_dist _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_chem_comp_bond.value_dist' _item.category_id chem_comp_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_bond.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_bond.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_bond.value_dist. ; _item.name '_chem_comp_bond.value_dist_esd' _item.category_id chem_comp_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_bond.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_CHIR ## #################### save_chem_comp_chir _category.description ; Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category. ; _category.id chem_comp_chir _category.mandatory_code no loop_ _category_key.name '_chem_comp_chir.comp_id' '_chem_comp_chir.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id phe phe1 CA val val1 CA # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_chir.atom_id _item_description.description ; The ID of the atom that is a chiral centre. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_chir.atom_id' _item.mandatory_code yes save_ save__chem_comp_chir.atom_config _item_description.description ; The chiral configuration of the atom that is a chiral centre. ; _item.name '_chem_comp_chir.atom_config' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail R 'absolute configuration R' S 'absolute configuration S' save_ save__chem_comp_chir.id _item_description.description ; The value of _chem_comp_chir.id must uniquely identify a record in the CHEM_COMP_CHIR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_chir.id' chem_comp_chir yes '_chem_comp_chir_atom.chir_id' chem_comp_chir_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_chir_atom.chir_id' '_chem_comp_chir.id' _item_type.code code save_ save__chem_comp_chir.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_chir.comp_id' _item.mandatory_code yes save_ save__chem_comp_chir.number_atoms_all _item_description.description ; The total number of atoms bonded to the atom specified by _chem_comp_chir.atom_id. ; _item.name '_chem_comp_chir.number_atoms_all' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code int save_ save__chem_comp_chir.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms bonded to the atom specified by _chem_comp_chir.atom_id. ; _item.name '_chem_comp_chir.number_atoms_nh' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code int save_ save__chem_comp_chir.volume_flag _item_description.description ; A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. ; _item.name '_chem_comp_chir.volume_flag' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sign 'match magnitude and sign' nosign 'match magnitude only' save_ save__chem_comp_chir.volume_three _item_description.description ; The chiral volume, V~c~, for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product ; _item.name '_chem_comp_chir.volume_three' _item.category_id chem_comp_chir _item.mandatory_code no _item_related.related_name '_chem_comp_chir.volume_three_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__chem_comp_chir.volume_three_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_chir.volume_three. ; _item.name '_chem_comp_chir.volume_three_esd' _item.category_id chem_comp_chir _item.mandatory_code no _item_related.related_name '_chem_comp_chir.volume_three' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ ######################### ## CHEM_COMP_CHIR_ATOM ## ######################### save_chem_comp_chir_atom _category.description ; Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component. ; _category.id chem_comp_chir_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_chir_atom.chir_id' '_chem_comp_chir_atom.atom_id' '_chem_comp_chir_atom.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_chir_atom.comp_id _chem_comp_chir_atom.chir_id _chem_comp_chir_atom.atom_id phe 1 N phe 1 C phe 1 CB val 1 N val 1 C val 1 CB # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_chir_atom.atom_id _item_description.description ; The ID of an atom bonded to the chiral atom. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_chir_atom.atom_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.chir_id _item_description.description ; This data item is a pointer to _chem_comp_chir.id in the CHEM_COMP_CHIR category. ; _item.name '_chem_comp_chir_atom.chir_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_chir_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.dev _item_description.description ; The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. ; _item.name '_chem_comp_chir_atom.dev' _item.category_id chem_comp_chir_atom _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_LINK ## #################### save_chem_comp_link _category.description ; Data items in the CHEM_COMP_LINK category give details about the links between chemical components. ; _category.id chem_comp_link _category.mandatory_code no _category_key.name '_chem_comp_link.link_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' # loop_ # _category_examples.detail # _category_examples.case # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ; # Example 1 - from nucleotide external reference dictionary Nucleic # Database Project 1997. # ; # ; # _chem_comp_link.link_id ribose_adenine # _chem_comp_link.type_comp_1 ribose # _chem_comp_link.type_comp_2 adenine # _chem_comp_link.details # ; # Defines the linkage between adenine base and ribose sugar # ; # ; # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_link.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_comp_link.link_id' _item.mandatory_code yes save_ save__chem_comp_link.details _item_description.description ; A description of special aspects of a link between chemical components in the structure. ; _item.name '_chem_comp_link.details' _item.category_id chem_comp_link _item.mandatory_code no _item_type.code text save_ save__chem_comp_link.type_comp_1 _item_description.description ; The type of the first of the two components joined by the link. This data item is a pointer to _chem_comp.type in the CHEM_COMP category. ; _item.name '_chem_comp_link.type_comp_1' _item.mandatory_code yes save_ save__chem_comp_link.type_comp_2 _item_description.description ; The type of the second of the two components joined by the link. This data item is a pointer to _chem_comp.type in the CHEM_COMP category. ; _item.name '_chem_comp_link.type_comp_2' _item.mandatory_code yes save_ ##################### ## CHEM_COMP_PLANE ## ##################### save_chem_comp_plane _category.description ; Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category. ; _category.id chem_comp_plane _category.mandatory_code no loop_ _category_key.name '_chem_comp_plane.comp_id' '_chem_comp_plane.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_plane.comp_id _chem_comp_plane.id phe phe1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_plane.id _item_description.description ; The value of _chem_comp_plane.id must uniquely identify a record in the CHEM_COMP_PLANE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_plane.id' chem_comp_plane yes '_chem_comp_plane_atom.plane_id' chem_comp_plane_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_plane_atom.plane_id' '_chem_comp_plane.id' _item_type.code code save_ save__chem_comp_plane.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_plane.comp_id' _item.mandatory_code yes save_ save__chem_comp_plane.number_atoms_all _item_description.description ; The total number of atoms in the plane. ; _item.name '_chem_comp_plane.number_atoms_all' _item.category_id chem_comp_plane _item.mandatory_code no _item_type.code int save_ save__chem_comp_plane.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_chem_comp_plane.number_atoms_nh' _item.category_id chem_comp_plane _item.mandatory_code no _item_type.code int save_ ########################## ## CHEM_COMP_PLANE_ATOM ## ########################## save_chem_comp_plane_atom _category.description ; Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component. ; _category.id chem_comp_plane_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_plane_atom.plane_id' '_chem_comp_plane_atom.atom_id' '_chem_comp_plane_atom.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.atom_id phe1 phe CB phe1 phe CG phe1 phe CD1 phe1 phe CE1 phe1 phe CZ phe1 phe CE2 phe1 phe CD2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_plane_atom.atom_id _item_description.description ; The ID of an atom involved in the plane. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_plane_atom.atom_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_plane_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.plane_id _item_description.description ; This data item is a pointer to _chem_comp_plane.id in the CHEM_COMP_PLANE category. ; _item.name '_chem_comp_plane_atom.plane_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.dist_esd _item_description.description ; This data item is the standard deviation of the out-of-plane distance for this atom. ; _item.name '_chem_comp_plane_atom.dist_esd' _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_TOR ## #################### save_chem_comp_tor _category.description ; Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category. ; _category.id chem_comp_tor _category.mandatory_code no loop_ _category_key.name '_chem_comp_tor.comp_id' '_chem_comp_tor.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 phe phe_chi1 N CA CB CG phe phe_chi2 CA CB CG CD1 phe phe_ring1 CB CG CD1 CE1 phe phe_ring2 CB CG CD2 CE2 phe phe_ring3 CG CD1 CE1 CZ phe phe_ring4 CD1 CE1 CZ CE2 phe phe_ring5 CE1 CZ CE2 CD2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_tor.atom_id_1 _item_description.description ; The ID of the first of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_3' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_2 _item_description.description ; The ID of the second of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_3' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_3 _item_description.description ; The ID of the third of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_4 _item_description.description ; The ID of the fourth of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_4' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_3' save_ save__chem_comp_tor.id _item_description.description ; The value of _chem_comp_tor.id must uniquely identify a record in the CHEM_COMP_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_tor.id' chem_comp_tor yes '_chem_comp_tor_value.tor_id' chem_comp_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_tor_value.tor_id' '_chem_comp_tor.id' _item_type.code code save_ save__chem_comp_tor.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_tor.comp_id' _item.mandatory_code yes save_ ########################## ## CHEM_COMP_TOR_VALUE ## ########################## save_chem_comp_tor_value _category.description ; Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. ; _category.id chem_comp_tor_value _category.mandatory_code no loop_ _category_key.name '_chem_comp_tor_value.tor_id' '_chem_comp_tor_value.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_tor_value.tor_id _chem_comp_tor_value.comp_id _chem_comp_tor_value.angle _chem_comp_tor_value.dist phe_chi1 phe -60.0 2.88 phe_chi1 phe 180.0 3.72 phe_chi1 phe 60.0 2.88 phe_chi2 phe 90.0 3.34 phe_chi2 phe -90.0 3.34 phe_ring1 phe 180.0 3.75 phe_ring2 phe 180.0 3.75 phe_ring3 phe 0.0 2.80 phe_ring4 phe 0.0 2.80 phe_ring5 phe 0.0 2.80 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_tor_value.comp_id _item_description.description ; This data item is a pointer to _chem_comp_atom.comp_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor_value.comp_id' _item.mandatory_code yes save_ save__chem_comp_tor_value.tor_id _item_description.description ; This data item is a pointer to _chem_comp_tor.id in the CHEM_COMP_TOR category. ; _item.name '_chem_comp_tor_value.tor_id' _item.mandatory_code yes save_ save__chem_comp_tor_value.angle _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_comp_tor_value.angle' _item.category_id chem_comp_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_comp_tor_value.angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_comp_tor_value.angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_tor_value.angle. ; _item.name '_chem_comp_tor_value.angle_esd' _item.category_id chem_comp_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_comp_tor_value.angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_comp_tor_value.dist _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. ; _item.name '_chem_comp_tor_value.dist' _item.category_id chem_comp_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_tor_value.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_tor_value.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_tor_value.dist. ; _item.name '_chem_comp_tor_value.dist_esd' _item.category_id chem_comp_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_tor_value.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ############### ## CHEM_LINK ## ############### save_chem_link _category.description ; Data items in the CHEM_LINK category give details about the links between chemical components. ; _category.id chem_link _category.mandatory_code no _category_key.name '_chem_link.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link.id _item_description.description ; The value of _chem_link.id must uniquely identify each item in the CHEM_LINK list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link.id' chem_link yes '_chem_link_angle.link_id' chem_link_angle yes '_chem_link_bond.link_id' chem_link_bond yes '_chem_link_chir.link_id' chem_link_chir yes '_chem_link_plane.link_id' chem_link_plane yes '_chem_link_tor.link_id' chem_link_tor yes '_chem_comp_link.link_id' chem_comp_link yes '_entity_link.link_id' entity_link yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_angle.link_id' '_chem_link.id' '_chem_link_bond.link_id' '_chem_link.id' '_chem_link_chir.link_id' '_chem_link.id' '_chem_link_plane.link_id' '_chem_link.id' '_chem_link_tor.link_id' '_chem_link.id' '_chem_comp_link.link_id' '_chem_link.id' '_entity_link.link_id' '_chem_link.id' _item_type.code code loop_ _item_examples.case 'peptide' 'oligosaccharide 1,4' 'DNA' save_ save__chem_link.details _item_description.description ; A description of special aspects of a link between chemical components in the structure. ; _item.name '_chem_link.details' _item.category_id chem_link _item.mandatory_code no _item_type.code text save_ ##################### ## CHEM_LINK_ANGLE ## ##################### save_chem_link_angle _category.description ; Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components. ; _category.id chem_link_angle _category.mandatory_code no loop_ _category_key.name '_chem_link_angle.link_id' '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_2' '_chem_link_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. ; ; loop_ _chem_link_angle.link_id _chem_link_angle.value_angle _chem_link_angle.value_angle_esd _chem_link_angle.atom_id_1 _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.atom_3_comp_id PEPTIDE 111.2 2.8 N 1 CA 1 C 1 PEPTIDE 120.8 1.7 CA 1 C 1 O 1 PEPTIDE 116.2 2.0 CA 1 C 1 N 2 PEPTIDE 123.0 1.6 O 1 C 1 N 2 PEPTIDE 121.7 1.8 C 1 N 2 CA 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_angle.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_angle.atom_1_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_2_comp_id' '_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_angle.atom_2_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_1_comp_id' '_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_3_comp_id _item_description.description ; This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_angle.atom_3_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_1_comp_id' '_chem_link_angle.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_id_1 _item_description.description ; The ID of the first of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_1_comp_id). ; _item.name '_chem_link_angle.atom_id_1' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_2' '_chem_link_angle.atom_id_3' _item_type.code code save_ save__chem_link_angle.atom_id_2 _item_description.description ; The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_2_comp_id). ; _item.name '_chem_link_angle.atom_id_2' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_3' _item_type.code code save_ save__chem_link_angle.atom_id_3 _item_description.description ; The ID of the third of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_3_comp_id). ; _item.name '_chem_link_angle.atom_id_3' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_2' _item_type.code code save_ save__chem_link_angle.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_angle.link_id' _item.mandatory_code yes save_ save__chem_link_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_link_angle.value_angle' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_link_angle.value_angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_angle.value_angle. ; _item.name '_chem_link_angle.value_angle_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_link_angle.value_dist _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_chem_link_angle.value_dist' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_angle.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_dist. ; _item.name '_chem_link_angle.value_dist_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_LINK_BOND ## #################### save_chem_link_bond _category.description ; Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure. ; _category.id chem_link_bond _category.mandatory_code no loop_ _category_key.name '_chem_link_bond.link_id' '_chem_link_bond.atom_id_1' '_chem_link_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. ; ; loop_ _chem_link_bond.link_id _chem_link_bond.value_dist _chem_link_bond.value_dist_esd _chem_link_bond.atom_id_1 _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.atom_2_comp_id PEPTIDE 1.458 0.019 N 1 CA 1 PEPTIDE 1.525 0.021 CA 1 C 1 PEPTIDE 1.329 0.014 C 1 N 2 PEPTIDE 1.231 0.020 C 1 O 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_bond.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_bond.atom_1_comp_id' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_bond.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_bond.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link. ; _item.name '_chem_link_bond.atom_2_comp_id' _item.category_id chem_link_bond _item.mandatory_code no _item_dependent.dependent_name '_chem_link_bond.atom_1_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_bond.atom_id_1 _item_description.description ; The ID of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_bond.atom_id_1' _item.category_id chem_link_bond _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_bond.atom_id_2' _item_type.code code save_ save__chem_link_bond.atom_id_2 _item_description.description ; The ID of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_chem_link_bond.atom_id_2' _item.category_id chem_link_bond _item.mandatory_code yes _item_dependent.dependent_name '_chem_link_bond.atom_id_1' _item_type.code code save_ save__chem_link_bond.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_bond.link_id' _item.mandatory_code yes save_ save__chem_link_bond.value_dist _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_chem_link_bond.value_dist' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_bond.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_bond.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_bond.value_dist. ; _item.name '_chem_link_bond.value_dist_esd' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_bond.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__chem_link_bond.value_order _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_chem_link_bond.value_order' _item.category_id chem_link_bond _item.mandatory_code no _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' save_ #################### ## CHEM_LINK_CHIR ## #################### save_chem_link_chir _category.description ; Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. ; _category.id chem_link_chir _category.mandatory_code no loop_ _category_key.name '_chem_link_chir.link_id' '_chem_link_chir.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_chir.atom_comp_id _item_description.description ; This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_chir.atom_comp_id' _item.category_id chem_link_chir _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_chir.atom_id _item_description.description ; The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_chir.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_chir.atom_config _item_description.description ; The chiral configuration of the atom that is a chiral centre. ; _item.name '_chem_link_chir.atom_config' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail R 'absolute configuration R' S 'absolute configuration S' save_ save__chem_link_chir.id _item_description.description ; The value of _chem_link_chir.id must uniquely identify a record in the CHEM_LINK_CHIR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_chir.id' chem_link_chir yes '_chem_link_chir_atom.chir_id' chem_link_chir_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_chir_atom.chir_id' '_chem_link_chir.id' _item_type.code code save_ save__chem_link_chir.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_chir.link_id' _item.mandatory_code yes save_ save__chem_link_chir.number_atoms_all _item_description.description ; The total number of atoms bonded to the atom specified by _chem_link_chir.atom_id. ; _item.name '_chem_link_chir.number_atoms_all' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code int save_ save__chem_link_chir.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms bonded to the atom specified by _chem_link_chir.atom_id. ; _item.name '_chem_link_chir.number_atoms_nh' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code int save_ save__chem_link_chir.volume_flag _item_description.description ; A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. ; _item.name '_chem_link_chir.volume_flag' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sign 'match magnitude and sign' nosign 'match magnitude only' save_ save__chem_link_chir.volume_three _item_description.description ; The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_link_chir.atom_id to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_link_chir.atom_id to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_link_chir.atom_id to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product ; _item.name '_chem_link_chir.volume_three' _item.category_id chem_link_chir _item.mandatory_code no _item_related.related_name '_chem_link_chir.volume_three_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__chem_link_chir.volume_three_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_chir.volume_three. ; _item.name '_chem_link_chir.volume_three_esd' _item.category_id chem_link_chir _item.mandatory_code no _item_related.related_name '_chem_link_chir.volume_three' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ ######################### ## CHEM_LINK_CHIR_ATOM ## ######################### save_chem_link_chir_atom _category.description ; Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components. ; _category.id chem_link_chir_atom _category.mandatory_code no loop_ _category_key.name '_chem_link_chir_atom.chir_id' '_chem_link_chir_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_chir_atom.atom_comp_id _item_description.description ; This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_chir_atom.atom_comp_id' _item.category_id chem_link_chir_atom _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_chir_atom.atom_id _item_description.description ; The ID of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_chir_atom.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_chir_atom.chir_id _item_description.description ; This data item is a pointer to _chem_link_chir.id in the CHEM_LINK_CHIR category. ; _item.name '_chem_link_chir_atom.chir_id' _item.mandatory_code yes save_ save__chem_link_chir_atom.dev _item_description.description ; The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. ; _item.name '_chem_link_chir_atom.dev' _item.category_id chem_link_chir_atom _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ ##################### ## CHEM_LINK_PLANE ## ##################### save_chem_link_plane _category.description ; Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. ; _category.id chem_link_plane _category.mandatory_code no loop_ _category_key.name '_chem_link_plane.link_id' '_chem_link_plane.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_plane.id _item_description.description ; The value of _chem_link_plane.id must uniquely identify a record in the CHEM_LINK_PLANE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_plane.id' chem_link_plane yes '_chem_link_plane_atom.plane_id' chem_link_plane_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_plane_atom.plane_id' '_chem_link_plane.id' _item_type.code code save_ save__chem_link_plane.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_plane.link_id' _item.mandatory_code yes save_ save__chem_link_plane.number_atoms_all _item_description.description ; The total number of atoms in the plane. ; _item.name '_chem_link_plane.number_atoms_all' _item.category_id chem_link_plane _item.mandatory_code no _item_type.code int save_ save__chem_link_plane.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_chem_link_plane.number_atoms_nh' _item.category_id chem_link_plane _item.mandatory_code no _item_type.code int save_ ########################## ## CHEM_LINK_PLANE_ATOM ## ########################## save_chem_link_plane_atom _category.description ; Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components. ; _category.id chem_link_plane_atom _category.mandatory_code no loop_ _category_key.name '_chem_link_plane_atom.plane_id' '_chem_link_plane_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_plane_atom.atom_comp_id _item_description.description ; This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_plane_atom.atom_comp_id' _item.category_id chem_link_plane_atom _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_plane_atom.atom_id _item_description.description ; The ID of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_plane_atom.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_plane_atom.plane_id _item_description.description ; This data item is a pointer to _chem_link_plane.id in the CHEM_LINK_PLANE category. ; _item.name '_chem_link_plane_atom.plane_id' _item.mandatory_code yes save_ ################### ## CHEM_LINK_TOR ## ################### save_chem_link_tor _category.description ; Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category. ; _category.id chem_link_tor _category.mandatory_code no loop_ _category_key.name '_chem_link_tor.link_id' '_chem_link_tor.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_tor.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_1_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_3_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_2_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_3_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_3_comp_id _item_description.description ; This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_3_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_4_comp_id _item_description.description ; This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_4_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_id_1 _item_description.description ; The ID of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_3' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_2 _item_description.description ; The ID of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_3' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_3 _item_description.description ; The ID of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_4 _item_description.description ; The ID of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_4' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_3' _item_type.code code save_ save__chem_link_tor.id _item_description.description ; The value of _chem_link_tor.id must uniquely identify a record in the CHEM_LINK_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_tor.id' chem_link_tor yes '_chem_link_tor_value.tor_id' chem_link_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_tor_value.tor_id' '_chem_link_tor.id' _item_type.code code save_ save__chem_link_tor.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_tor.link_id' _item.mandatory_code yes save_ ######################### ## CHEM_LINK_TOR_VALUE ## ######################### save_chem_link_tor_value _category.description ; Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. ; _category.id chem_link_tor_value _category.mandatory_code no _category_key.name '_chem_link_tor_value.tor_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_tor_value.tor_id _item_description.description ; This data item is a pointer to _chem_link_tor.id in the CHEM_LINK_TOR category. ; _item.name '_chem_link_tor_value.tor_id' _item.mandatory_code yes save_ save__chem_link_tor_value.angle _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_link_tor_value.angle' _item.category_id chem_link_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_link_tor_value.angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_link_tor_value.angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_tor_value.angle. ; _item.name '_chem_link_tor_value.angle_esd' _item.category_id chem_link_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_link_tor_value.angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_link_tor_value.dist _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. ; _item.name '_chem_link_tor_value.dist' _item.category_id chem_link_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_tor_value.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_tor_value.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_tor_value.dist. ; _item.name '_chem_link_tor_value.dist_esd' _item.category_id chem_link_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_tor_value.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ############## ## CHEMICAL ## ############## save_chemical _category.description ; Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. ; _category.id chemical _category.mandatory_code no _category_key.name '_chemical.entry_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. ; ; _chemical.entry_id '9597gaus' _chemical.name_systematic trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0) ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_chemical.entry_id' _item.mandatory_code yes save_ save__chemical.compound_source _item_description.description ; Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. ; _item.name '_chemical.compound_source' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_compound_source' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'From Norilsk (USSR)' 'Extracted from the bark of Cinchona Naturalis' save_ save__chemical.melting_point _item_description.description ; The temperature in kelvins at which the crystalline solid changes to a liquid. ; _item.name '_chemical.melting_point' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_melting_point' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code kelvins save_ save__chemical.name_common _item_description.description ; Trivial name by which the compound is commonly known. ; _item.name '_chemical.name_common' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_common' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '1-bromoestradiol' save_ save__chemical.name_mineral _item_description.description ; Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also _chemical.compound_source. ; _item.name '_chemical.name_mineral' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_mineral' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'chalcopyrite' save_ save__chemical.name_structure_type _item_description.description ; Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. ; _item.name '_chemical.name_structure_type' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_structure_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'perovskite' 'sphalerite' 'A15' save_ save__chemical.name_systematic _item_description.description ; IUPAC or Chemical Abstracts full name of the compound. ; _item.name '_chemical.name_systematic' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_systematic' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '1-bromoestra-1,3,5(10)-triene-3,17\b-diol' save_ ######################## ## CHEMICAL_CONN_ATOM ## ######################## save_chemical_conn_atom _category.description ; Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. ; _category.id chemical_conn_atom _category.mandatory_code no _category_key.name '_chemical_conn_atom.number' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. ; ; loop_ _chemical_conn_atom.number _chemical_conn_atom.type_symbol _chemical_conn_atom.display_x _chemical_conn_atom.display_y _chemical_conn_atom.NCA _chemical_conn_atom.NH 1 S .39 .81 1 0 2 S .39 .96 2 0 3 N .14 .88 3 0 4 C .33 .88 3 0 5 C .11 .96 2 2 6 C .03 .96 2 2 7 C .03 .80 2 2 8 C .11 .80 2 2 9 S .54 .81 1 0 10 S .54 .96 2 0 11 N .80 .88 3 0 12 C .60 .88 3 0 13 C .84 .96 2 2 14 C .91 .96 2 2 15 C .91 .80 2 2 16 C .84 .80 2 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_conn_atom.charge _item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chemical_conn_atom.charge' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_charge' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 -8 -8 -8 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' save_ save__chemical_conn_atom.display_x _item_description.description ; The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. ; _item.name '_chemical_conn_atom.display_x' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_x' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_atom.display_y' loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__chemical_conn_atom.display_y _item_description.description ; The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. ; _item.name '_chemical_conn_atom.display_y' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_y' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_atom.display_x' loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__chemical_conn_atom.NCA _item_description.description ; The number of connected atoms excluding terminal hydrogen atoms. ; _item.name '_chemical_conn_atom.NCA' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NCA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__chemical_conn_atom.NH _item_description.description ; The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as _atom_site.attached_hydrogens only if none of the hydrogen atoms appear in the ATOM_SITE list. ; _item.name '_chemical_conn_atom.NH' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NH' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__chemical_conn_atom.number _item_description.description ; The chemical sequence number to be associated with this atom. Within an ATOM_SITE list, this number must match one of the _atom_site.chemical_conn_number values. ; loop_ _item.name _item.category_id _item.mandatory_code '_chemical_conn_atom.number' chemical_conn_atom yes '_atom_site.chemical_conn_number' atom_site no '_chemical_conn_bond.atom_1' chemical_conn_bond yes '_chemical_conn_bond.atom_2' chemical_conn_bond yes _item_aliases.alias_name '_chemical_conn_atom_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.chemical_conn_number' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_1' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_2' '_chemical_conn_atom.number' loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__chemical_conn_atom.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_chemical_conn_atom.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_atom_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ ######################## ## CHEMICAL_CONN_BOND ## ######################## save_chemical_conn_bond _category.description ; Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms. ; _category.id chemical_conn_bond _category.mandatory_code no loop_ _category_key.name '_chemical_conn_bond.atom_1' '_chemical_conn_bond.atom_2' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. ; ; loop_ _chemical_conn_bond.atom_1 _chemical_conn_bond.atom_2 _chemical_conn_bond.type 4 1 doub 4 3 sing 4 2 sing 5 3 sing 6 5 sing 7 6 sing 8 7 sing 8 3 sing 10 2 sing 12 9 doub 12 11 sing 12 10 sing 13 11 sing 14 13 sing 15 14 sing 16 15 sing 16 11 sing 17 5 sing 18 5 sing 19 6 sing 20 6 sing 21 7 sing 22 7 sing 23 8 sing 24 8 sing 25 13 sing 26 13 sing 27 14 sing 28 14 sing 29 15 sing 30 15 sing 31 16 sing 32 16 sing ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_conn_bond.atom_1 _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_chemical_conn_bond.atom_1' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_bond_atom_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_bond.atom_2' save_ save__chemical_conn_bond.atom_2 _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_chemical_conn_bond.atom_2' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_bond_atom_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_bond.atom_1' save_ save__chemical_conn_bond.type _item_description.description ; The chemical bond type associated with the connection between the two sites _chemical_conn_bond.atom_1 and _chemical_conn_bond.atom_2. ; _item.name '_chemical_conn_bond.type' _item.category_id chemical_conn_bond _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_bond_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' save_ ###################### ## CHEMICAL_FORMULA ## ###################### save_chemical_formula _category.description ; Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and _chemical_formula.sum. For the data item _chemical_formula.moiety, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula.moiety). (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for _chemical_formula.moiety formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula.structural, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. ; _category.id chemical_formula _category.mandatory_code no _category_key.name '_chemical_formula.entry_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _chemical_formula.entry_id 'TOZ' _chemical_formula.moiety 'C18 H25 N O3' _chemical_formula.sum 'C18 H25 N O3' _chemical_formula.weight 303.40 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_formula.analytical _item_description.description ; Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (estimated standard deviations). ; _item.name '_chemical_formula.analytical' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_analytical' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Fe2.45(2) Ni1.60(3) S4' save_ save__chemical_formula.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_chemical_formula.entry_id' _item.mandatory_code yes save_ save__chemical_formula.iupac _item_description.description ; Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other CHEMICAL_FORMULA entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other CHEMICAL_FORMULA data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. ; _item.name '_chemical_formula.iupac' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_iupac' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' save_ save__chemical_formula.moiety _item_description.description ; Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: (1) Moieties are separated by commas ','. (2) The order of elements within a moiety follows general rule (5) in the CHEMICAL_FORMULA category description. (3) Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. (4) Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. ; _item.name '_chemical_formula.moiety' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_moiety' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'C7 H4 Cl Hg N O3 S' 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-' 'C12 H16 N2 O6, 5(H2 O1)' "(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)" save_ save__chemical_formula.structural _item_description.description ; See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom-type and atom-site data should not be included in this formula (see also _chemical_formula.analytical). ; _item.name '_chemical_formula.structural' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_structural' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Ca ((Cl O3)2 O)2 (H2 O)6' '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' save_ save__chemical_formula.sum _item_description.description ; See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule (5) in the CHEMICAL_FORMULA category description. Parentheses are not normally used. ; _item.name '_chemical_formula.sum' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_sum' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'C18 H19 N7 O8 S' save_ save__chemical_formula.weight _item_description.description ; Formula mass in daltons. This mass should correspond to the formulae given under _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum and, together with the Z value and cell parameters, should yield the density given as _exptl_crystal.density_diffrn. ; _item.name '_chemical_formula.weight' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__chemical_formula.weight_meas _item_description.description ; Formula mass in daltons measured by a non-diffraction experiment. ; _item.name '_chemical_formula.weight_meas' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ ############## ## CITATION ## ############## save_citation _category.description ; Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block. ; _category.id citation _category.mandatory_code no _category_key.name '_citation.id' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _citation.id _citation.coordinate_linkage _citation.title _citation.country _citation.journal_abbrev _citation.journal_volume _citation.journal_issue _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_title _citation.book_publisher _citation.book_id_ISBN _citation.details primary yes ; Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution. ; US 'J. Biol. Chem.' 265 . 14209 14219 1990 HBCHA3 0021-9258 071 . . . ; The publication that directly relates to this coordinate set. ; 2 no ; Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1. ; UK 'Nature' 337 . 615 619 1989 NATUAS 0028-0836 006 . . . ; Determination of the structure of the unliganded enzyme. ; 3 no ; Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1. ; US 'J. Biol. Chem.' 264 . 1919 1921 1989 HBCHA3 0021-9258 071 . . . ; Crystallization of the unliganded enzyme. ; 4 no ; Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease. ; US 'J. Biol. Chem.' 264 . 2307 2312 1989 HBCHA3 0021-9258 071 . . . ; Expression and purification of the enzyme. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation.abstract _item_description.description ; Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. ; _item.name '_citation.abstract' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_abstract' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__citation.abstract_id_CAS _item_description.description ; The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. ; _item.name '_citation.abstract_id_CAS' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_abstract_id_CAS' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__citation.book_id_ISBN _item_description.description ; The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. ; _item.name '_citation.book_id_ISBN' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_id_ISBN' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.book_publisher _item_description.description ; The name of the publisher of the citation; relevant for books or book chapters. ; _item.name '_citation.book_publisher' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_publisher' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'John Wiley and Sons' save_ save__citation.book_publisher_city _item_description.description ; The location of the publisher of the citation; relevant for books or book chapters. ; _item.name '_citation.book_publisher_city' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_publisher_city' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'London' save_ save__citation.book_title _item_description.description ; The title of the book in which the citation appeared; relevant for books or book chapters. ; _item.name '_citation.book_title' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__citation.coordinate_linkage _item_description.description ; _citation.coordinate_linkage states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'. ; _item.name '_citation.coordinate_linkage' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_coordinate_linkage' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'citation unrelated to current coordinates' n 'abbreviation for "no"' yes 'citation related to current coordinates' y 'abbreviation for "yes"' save_ save__citation.country _item_description.description ; The country of publication; relevant for books and book chapters. ; _item.name '_citation.country' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_country' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.database_id_Medline _item_description.description ; Accession number used by Medline to categorize a specific bibliographic entry. ; _item.name '_citation.database_id_Medline' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_database_id_Medline' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int _item_examples.case 89064067 save_ save__citation.details _item_description.description ; A description of special aspects of the relationship of the contents of the data block to the literature item cited. ; _item.name '_citation.details' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case ; citation relates to this precise coordinate set ; ; citation relates to earlier low-resolution structure ; ; citation relates to further refinement of structure reported in citation 2 ; save_ save__citation.id _item_description.description ; The value of _citation.id must uniquely identify a record in the CITATION list. The _citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_citation.id' citation yes '_citation_author.citation_id' citation_author yes '_citation_editor.citation_id' citation_editor yes '_software.citation_id' software no _item_aliases.alias_name '_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_citation_author.citation_id' '_citation.id' '_citation_editor.citation_id' '_citation.id' '_software.citation_id' '_citation.id' _item_type.code code loop_ _item_examples.case 'primary' '1' '2' save_ save__citation.journal_abbrev _item_description.description ; Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. ; _item.name '_citation.journal_abbrev' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_abbrev' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'J. Mol. Biol.' save_ save__citation.journal_id_ASTM _item_description.description ; The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. ; _item.name '_citation.journal_id_ASTM' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ASTM' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.journal_id_CSD _item_description.description ; The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). ; _item.name '_citation.journal_id_CSD' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_CSD' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '0070' save_ save__citation.journal_id_ISSN _item_description.description ; The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. ; _item.name '_citation.journal_id_ISSN' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ISSN' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.journal_full _item_description.description ; Full name of the cited journal; relevant for journal articles. ; _item.name '_citation.journal_full' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_full' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Journal of Molecular Biology' save_ save__citation.journal_issue _item_description.description ; Issue number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_issue' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_issue' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '2' save_ save__citation.journal_volume _item_description.description ; Volume number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_volume' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_volume' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '174' save_ save__citation.language _item_description.description ; Language in which the cited article is written. ; _item.name '_citation.language' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_language' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'German' save_ save__citation.page_first _item_description.description ; The first page of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.page_first' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_first' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.page_last _item_description.description ; The last page of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.page_last' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_last' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.title _item_description.description ; The title of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.title' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Structure of diferric duck ovotransferrin at 2.35 \%A resolution. ; save_ save__citation.year _item_description.description ; The year of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.year' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_year' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int _item_examples.case 1984 save_ ##################### ## CITATION_AUTHOR ## ##################### save_citation_author _category.description ; Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. ; _category.id citation_author _category.mandatory_code no loop_ _category_key.name '_citation_author.citation_id' '_citation_author.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _citation_author.citation_id _citation_author.ordinal _citation_author.name primary 1 'Fitzgerald, P.M.D.' primary 2 'McKeever, B.M.' primary 3 'Van Middlesworth, J.F.' primary 4 'Springer, J.P.' primary 5 'Heimbach, J.C.' primary 6 'Leu, C.-T.' primary 7 'Herber, W.K.' primary 8 'Dixon, R.A.F.' primary 9 'Darke, P.L.' 2 1 'Navia, M.A.' 2 2 'Fitzgerald, P.M.D.' 2 3 'McKeever, B.M.' 2 4 'Leu, C.-T.' 2 5 'Heimbach, J.C.' 2 6 'Herber, W.K.' 2 7 'Sigal, I.S.' 2 8 'Darke, P.L.' 2 9 'Springer, J.P.' 3 1 'McKeever, B.M.' 3 2 'Navia, M.A.' 3 3 'Fitzgerald, P.M.D.' 3 4 'Springer, J.P.' 3 5 'Leu, C.-T.' 3 6 'Heimbach, J.C.' 3 7 'Herber, W.K.' 3 8 'Sigal, I.S.' 3 9 'Darke, P.L.' 4 1 'Darke, P.L.' 4 2 'Leu, C.-T.' 4 3 'Davis, L.J.' 4 4 'Heimbach, J.C.' 4 5 'Diehl, R.E.' 4 6 'Hill, W.S.' 4 7 'Dixon, R.A.F.' 4 8 'Sigal, I.S.' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation_author.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_citation_author.citation_id' _item.mandatory_code yes _item_aliases.alias_name '_citation_author_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__citation_author.name _item_description.description ; Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_citation_author.name' _item.category_id citation_author _item.mandatory_code yes _item_aliases.alias_name '_citation_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__citation_author.ordinal _item_description.description ; This data item defines the order of the author's name in the list of authors of a citation. ; _item.name '_citation_author.ordinal' _item.category_id citation_author _item.mandatory_code no _item_aliases.alias_name '_citation_author_ordinal' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ ##################### ## CITATION_EDITOR ## ##################### save_citation_editor _category.description ; Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list. ; _category.id citation_editor _category.mandatory_code no loop_ _category_key.name '_citation_editor.citation_id' '_citation_editor.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _citation_editor.citation_id _citation_editor.name 5 'McKeever, B.M.' 5 'Navia, M.A.' 5 'Fitzgerald, P.M.D.' 5 'Springer, J.P.' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation_editor.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_citation_editor.citation_id' _item.mandatory_code yes _item_aliases.alias_name '_citation_editor_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__citation_editor.name _item_description.description ; Names of an editor of the citation; relevant for books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_citation_editor.name' _item.category_id citation_editor _item.mandatory_code no _item_aliases.alias_name '_citation_editor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__citation_editor.ordinal _item_description.description ; This data item defines the order of the editor's name in the list of editors of a citation. ; _item.name '_citation_editor.ordinal' _item.category_id citation_editor _item.mandatory_code no _item_aliases.alias_name '_citation_editor_ordinal' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ ############### ## COMPUTING ## ############### save_computing _category.description ; Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead. ; _category.id computing _category.mandatory_code no _category_key.name '_computing.entry_id' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. ; ; _computing.data_collection 'CAD-4 (Enraf-Nonius, 1989)' _computing.cell_refinement 'CAD-4 (Enraf-Nonius, 1989)' _computing.data_reduction 'CFEO (Solans, 1978)' _computing.structure_solution 'SHELXS86 (Sheldrick, 1990)' _computing.structure_refinement 'SHELXL93 (Sheldrick, 1993)' _computing.molecular_graphics 'ORTEPII (Johnson, 1976)' _computing.publication_material 'PARST (Nardelli, 1983)' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__computing.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_computing.entry_id' _item.mandatory_code yes save_ save__computing.cell_refinement _item_description.description ; Software used for cell refinement. Give the program or package name and a brief reference. ; _item.name '_computing.cell_refinement' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_cell_refinement' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'CAD4 (Enraf-Nonius, 1989)' save_ save__computing.data_collection _item_description.description ; Software used for data collection. Give the program or package name and a brief reference. ; _item.name '_computing.data_collection' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_data_collection' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'CAD4 (Enraf-Nonius, 1989)' save_ save__computing.data_reduction _item_description.description ; Software used for data reduction. Give the program or package name and a brief reference. ; _item.name '_computing.data_reduction' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_data_reduction' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)' save_ save__computing.molecular_graphics _item_description.description ; Software used for molecular graphics. Give the program or package name and a brief reference. ; _item.name '_computing.molecular_graphics' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_molecular_graphics' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'FRODO (Jones, 1986), ORTEP (Johnson, 1965)' save_ save__computing.publication_material _item_description.description ; Software used for generating material for publication. Give the program or package name and a brief reference. ; _item.name '_computing.publication_material' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_publication_material' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__computing.structure_refinement _item_description.description ; Software used for refinement of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_refinement' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_structure_refinement' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'SHELX85 (Sheldrick, 1985)' 'X-PLOR (Brunger, 1992)' save_ save__computing.structure_solution _item_description.description ; Software used for solution of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_solution' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_structure_solution' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'SHELX85 (Sheldrick, 1985)' save_ ############## ## DATABASE ## ############## save_database _category.description ; Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs. ; _category.id database _category.mandatory_code no _category_key.name '_database.entry_id' loop_ _category_group.id 'inclusive_group' 'compliance_group' save_ save__database.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_database.entry_id' _item.mandatory_code yes save_ #save__database.code_CAS # _item_description.description #; The code assigned by Chemical Abstracts. #; # _item.name '_database.code_CAS' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_CAS' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_CSD # _item_description.description #; The code assigned by the Cambridge Structural Database # (organic and metal-organic compounds). #; # _item.name '_database.code_CSD' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_CSD' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_ICSD # _item_description.description #; The code assigned by the Inorganic Crystal Structure Database. #; # _item.name '_database.code_ICSD' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_ICSD' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_MDF # _item_description.description #; The code assigned by the Metals Data File (metal structures). #; # _item.name '_database.code_MDF' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_MDF' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_NBS # _item_description.description #; The code assigned by the NBS (NIST) Crystal Data Database # (lattice parameters). #; # _item.name '_database.code_NBS' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_NBS' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_PDF # _item_description.description #; The code assigned by the Powder Diffraction File (JCPDS/ICDD). #; # _item.name '_database.code_PDF' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_PDF' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # save__database.journal_ASTM _item_description.description ; The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service. ; _item.name '_database.journal_ASTM' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_journal_ASTM' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__database.journal_CSD _item_description.description ; The journal code used in the Cambridge Structural Database. ; _item.name '_database.journal_CSD' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_journal_CSD' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ################ ## DATABASE_2 ## ################ save_database_2 _category.description ; Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created. ; _category.id database_2 _category.mandatory_code no loop_ _category_key.name '_database_2.database_id' '_database_2.database_code' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _database_2.database_id 'PDB' _database_2.database_code '5HVP' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_2.database_id _item_description.description ; An abbreviation that identifies the database. ; _item.name '_database_2.database_id' _item.category_id database_2 _item.mandatory_code yes loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' replaces '_database.code_CSD' replaces '_database.code_ICSD' replaces '_database.code_MDF' replaces '_database.code_NBS' replaces '_database.code_PDF' replaces _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail CAS ; Chemical Abstracts ; CSD ; Cambridge Structural Database (organic and metal-organic compounds) ; ICSD ; Inorganic Crystal Structure Database ; MDF ; Metals Data File (metal structures) ; NDB ; Nucleic Acid Database ; NBS ; NBS (NIST) Crystal Data Database (lattice parameters) ; PDB ; Protein Data Bank ; PDF ; Powder Diffraction File (JCPDS/ICDD) ; RCSB ; Research Collaboratory for Structural Bioinformatics ; EBI ; European Bioinformatics Institute ; save_ save__database_2.database_code _item_description.description ; The code assigned by the database identified in _database_2.database_id. ; _item.name '_database_2.database_code' _item.category_id database_2 _item.mandatory_code yes loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' replaces '_database.code_CSD' replaces '_database.code_ICSD' replaces '_database.code_MDF' replaces '_database.code_NBS' replaces '_database.code_PDF' replaces _item_type.code line loop_ _item_examples.case 1ABC ABCDEF save_ ######################### ## DATABASE_PDB_CAVEAT ## ######################### save_database_PDB_caveat _category.description ; Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_caveat _category.mandatory_code no _category_key.name '_database_PDB_caveat.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _database_PDB_caveat.id _database_PDB_caveat.text 1 ; THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS ; 2 ; UNCORRECTABLE AT THIS TIME ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_caveat.id _item_description.description ; A unique identifier for the PDB caveat record. ; _item.name '_database_PDB_caveat.id' _item.category_id database_PDB_caveat _item.mandatory_code yes _item_type.code int save_ save__database_PDB_caveat.text _item_description.description ; The full text of the PDB caveat record. ; _item.name '_database_PDB_caveat.text' _item.category_id database_PDB_caveat _item.mandatory_code no _item_type.code text save_ ######################### ## DATABASE_PDB_MATRIX ## ######################### save_database_PDB_matrix _category.description ; The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_matrix _category.mandatory_code no _category_key.name '_database_PDB_matrix.entry_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' save_ save__database_PDB_matrix.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_database_PDB_matrix.entry_id' _item.mandatory_code yes save_ save__database_PDB_matrix.origx[1][1] _item_description.description ; The [1][1] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[1][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[1][2] _item_description.description ; The [1][2] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[1][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[1][3] _item_description.description ; The [1][3] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[1][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[2][1] _item_description.description ; The [2][1] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[2][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[2][2] _item_description.description ; The [2][2] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[2][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[2][3] _item_description.description ; The [2][3] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[2][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[3][1] _item_description.description ; The [3][1] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[3][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[3][2] _item_description.description ; The [3][2] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[3][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[3][3] _item_description.description ; The [3][3] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[3][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx_vector[1] _item_description.description ; The [1] element of the PDB ORIGX vector. ; _item.name '_database_PDB_matrix.origx_vector[1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.origx_vector[2] _item_description.description ; The [2] element of the PDB ORIGX vector. ; _item.name '_database_PDB_matrix.origx_vector[2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.origx_vector[3] _item_description.description ; The [3] element of the PDB ORIGX vector. ; _item.name '_database_PDB_matrix.origx_vector[3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.scale[1][1] _item_description.description ; The [1][1] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[1][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[1][2] _item_description.description ; The [1][2] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[1][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[1][3] _item_description.description ; The [1][3] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[1][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[2][1] _item_description.description ; The [2][1] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[2][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[2][2] _item_description.description ; The [2][2] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[2][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[2][3] _item_description.description ; The [2][3] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[2][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[3][1] _item_description.description ; The [3][1] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[3][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[3][2] _item_description.description ; The [3][2] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[3][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[3][3] _item_description.description ; The [3][3] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[3][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale_vector[1] _item_description.description ; The [1] element of the PDB SCALE vector. ; _item.name '_database_PDB_matrix.scale_vector[1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.scale_vector[2] _item_description.description ; The [2] element of the PDB SCALE vector. ; _item.name '_database_PDB_matrix.scale_vector[2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.scale_vector[3] _item_description.description ; The [3] element of the PDB SCALE vector. ; _item.name '_database_PDB_matrix.scale_vector[3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ######################### ## DATABASE_PDB_REMARK ## ######################### save_database_PDB_remark _category.description ; Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_remark _category.mandatory_code no _category_key.name '_database_PDB_remark.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _database_PDB_remark.id _database_PDB_remark.text 3 ; REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE WEIGHTS OF THE CORRESPONDING RESTRAINTS) DISTANCE RESTRAINTS (ANGSTROMS) BOND DISTANCE 0.018(0.020) ANGLE DISTANCE 0.038(0.030) PLANAR 1-4 DISTANCE 0.043(0.040) PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) SINGLE TORSION CONTACT 0.216(0.500) MULTIPLE TORSION CONTACT 0.207(0.500) POSSIBLE HYDROGEN BOND 0.245(0.500) CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) PLANAR (OMEGA) 2.6(3.0) STAGGERED 17.4(15.0) ORTHONORMAL 18.1(20.0) ; 4 ; THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE THE CHAIN INDICATORS *A* AND *B*. ; # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_remark.id _item_description.description ; A unique identifier for the PDB remark record. ; _item.name '_database_PDB_remark.id' _item.category_id database_PDB_remark _item.mandatory_code yes _item_type.code int save_ save__database_PDB_remark.text _item_description.description ; The full text of the PDB remark record. ; _item.name '_database_PDB_remark.text' _item.category_id database_PDB_remark _item.mandatory_code no _item_type.code text save_ ###################### ## DATABASE_PDB_REV ## ###################### save_database_PDB_rev _category.description ; Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. ; _category.id database_PDB_rev _category.mandatory_code no _category_key.name '_database_PDB_rev.num' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _database_PDB_rev.num _database_PDB_rev.author_name _database_PDB_rev.date _database_PDB_rev.date_original _database_PDB_rev.status _database_PDB_rev.mod_type 1 'Fitzgerald, Paula M.D' 1991-10-15 1990-04-30 'full release' 0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_rev.author_name _item_description.description ; The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma precedes the first name(s) or initial(s). ; _item.name '_database_PDB_rev.author_name' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__database_PDB_rev.date _item_description.description ; Date the PDB revision took place. Taken from the REVDAT record. ; _item.name '_database_PDB_rev.date' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save__database_PDB_rev.date_original _item_description.description ; Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record. ; _item.name '_database_PDB_rev.date_original' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case '1980-08-21' save_ save__database_PDB_rev.mod_type _item_description.description ; Taken from the REVDAT record. Refer to the Protein Data Bank format description at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html for details. ; _item.name '_database_PDB_rev.mod_type' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code int loop_ _item_enumeration.value _item_enumeration.detail 0 'initial entry' 1 'all other types of modification' 2 'modifications to CONECT records' 3 ; modifications affecting the coordinates or their transforms (CRYST1, ORIGX, SCALE, MTRIX, TVECT, ATOM, HETATM, SIGATM records) ; 4 ; layer 1 to layer 2 revision which may affect all record types ; 5 'data uniformity processing' save_ save__database_PDB_rev.num _item_description.description ; The value of _database_PDB_rev.num must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number and that modification numbers are assigned in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_database_PDB_rev.num' database_PDB_rev yes '_database_PDB_rev_record.rev_num' database_PDB_rev_record yes loop_ _item_linked.child_name _item_linked.parent_name '_database_PDB_rev_record.rev_num' '_database_PDB_rev.num' _item_type.code int save_ save__database_PDB_rev.replaced_by _item_description.description ; The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. ; _item.name '_database_PDB_rev.replaced_by' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line save_ save__database_PDB_rev.replaces _item_description.description ; The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. ; _item.name '_database_PDB_rev.replaces' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line save_ save__database_PDB_rev.status _item_description.description ; The status of this revision. ; _item.name '_database_PDB_rev.status' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value 'in preparation' 'prerelease' 'full release' 'obsolete' save_ ############################# ## DATABASE_PDB_REV_RECORD ## ############################# save_database_PDB_rev_record _category.description ; Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. ; _category.id database_PDB_rev_record _category.mandatory_code no loop_ _category_key.name '_database_PDB_rev_record.rev_num' '_database_PDB_rev_record.type' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _database_PDB_rev_record.rev_num _database_PDB_rev_record.type _database_PDB_rev_record.details 1 CONECT ; Error fix - incorrect connection between atoms 2312 and 2317 ; 2 MATRIX 'For consistency with 1995-08-04 style-guide' 3 ORIGX 'Based on new data from author' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_rev_record.details _item_description.description ; A description of special aspects of the revision of records in this PDB entry. ; _item.name '_database_PDB_rev_record.details' _item.category_id database_PDB_rev_record _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Based on new data from author' 'For consistency with 1995-08-04 style-guide' 'For consistency with structural class' save_ save__database_PDB_rev_record.rev_num _item_description.description ; This data item is a pointer to _database_PDB_rev.num in the DATABASE_PDB_REV category. ; _item.name '_database_PDB_rev_record.rev_num' _item.mandatory_code yes save_ save__database_PDB_rev_record.type _item_description.description ; The types of records that were changed in this revision to a PDB entry. ; _item.name '_database_PDB_rev_record.type' _item.category_id database_PDB_rev_record _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'CRYST1' 'SCALE' 'MTRIX' 'ATOM' 'HETATM' save_ ######################## ## DATABASE_PDB_TVECT ## ######################## save_database_PDB_tvect _category.description ; The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file. ; _category.id database_PDB_tvect _category.mandatory_code no _category_key.name '_database_PDB_tvect.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' save_ save__database_PDB_tvect.details _item_description.description ; A description of special aspects of this TVECT. ; _item.name '_database_PDB_tvect.details' _item.category_id database_PDB_tvect _item.mandatory_code no _item_type.code text save_ save__database_PDB_tvect.id _item_description.description ; The value of _database_PDB_tvect.id must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_database_PDB_tvect.id' _item.category_id database_PDB_tvect _item.mandatory_code yes _item_type.code code save_ save__database_PDB_tvect.vector[1] _item_description.description ; The [1] element of the PDB TVECT vector. ; _item.name '_database_PDB_tvect.vector[1]' _item.category_id database_PDB_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_tvect.vector[2] _item_description.description ; The [2] element of the PDB TVECT vector. ; _item.name '_database_PDB_tvect.vector[2]' _item.category_id database_PDB_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_tvect.vector[3] _item_description.description ; The [3] element of the PDB TVECT vector. ; _item.name '_database_PDB_tvect.vector[3]' _item.category_id database_PDB_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ############ ## DIFFRN ## ############ save_diffrn _category.description ; Data items in the DIFFRN category record details about the diffraction data and their measurement. ; _category.id diffrn _category.mandatory_code no _category_key.name '_diffrn.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn.id 'Set1' _diffrn.ambient_temp 293(3) _diffrn.ambient_environment ; Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air ; _diffrn.crystal_support ; 0.7 mm glass capillary, sealed with dental wax ; _diffrn.crystal_treatment ; Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn.id 'd1' _diffrn.details ; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per min. Background counts for 5 sec on each side every scan. ; _diffrn.ambient_temp 293 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn.ambient_environment _item_description.description ; The gas or liquid surrounding the sample, if not air. ; _item.name '_diffrn.ambient_environment' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_environment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ #save__diffrn.ambient_pressure # _item_description.description #; The mean pressure in kilopascals at which the intensities were # measured. #; # _item.name '_diffrn.ambient_pressure' # _item.category_id diffrn # _item.mandatory_code no # _item_aliases.alias_name '_diffrn_ambient_pressure' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_related.related_name '_diffrn.ambient_pressure_esd' # _item_related.function_code associated_esd # _item_type.code float # _item_type_conditions.code esd # _item_units.code kilopascals # save_ # #save__diffrn.ambient_pressure_esd # _item_description.description #; The standard uncertainty (estimated standard deviation) # of _diffrn.ambient_pressure. #; # _item.name '_diffrn.ambient_pressure_esd' # _item.category_id diffrn # _item.mandatory_code no # _item_default.value 0.0 # _item_related.related_name '_diffrn.ambient_pressure' # _item_related.function_code associated_value # _item_type.code float # _item_units.code kilopascals # save_ save__diffrn.ambient_temp _item_description.description ; The mean temperature in kelvins at which the intensities were measured. ; _item.name '_diffrn.ambient_temp' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_temperature' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_diffrn.ambient_temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvins save_ save__diffrn.ambient_temp_details _item_description.description ; A description of special aspects of temperature control during data collection. ; _item.name '_diffrn.ambient_temp_details' _item.category_id diffrn _item.mandatory_code no _item_type.code text save_ save__diffrn.ambient_temp_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _diffrn.ambient_temp. ; _item.name '_diffrn.ambient_temp_esd' _item.category_id diffrn _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_diffrn.ambient_temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvins save_ save__diffrn.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_diffrn.crystal_id' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_crystal_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn.crystal_support _item_description.description ; The physical device used to support the crystal during data collection. ; _item.name '_diffrn.crystal_support' _item.category_id diffrn _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'glass capillary' 'quartz capillary' 'fiber' 'metal loop' save_ save__diffrn.crystal_treatment _item_description.description ; Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. ; _item.name '_diffrn.crystal_treatment' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_crystal_treatment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'equilibrated in hutch for 24 hours' 'flash frozen in liquid nitrogen' 'slow cooled with direct air stream' save_ save__diffrn.details _item_description.description ; Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. ; _item.name '_diffrn.details' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn.id _item_description.description ; This data item uniquely identifies a set of diffraction data. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn.id' diffrn yes '_diffrn_detector.diffrn_id' diffrn_detector yes '_diffrn_measurement.diffrn_id' diffrn_measurement yes '_diffrn_orient_matrix.diffrn_id' diffrn_orient_matrix yes '_diffrn_orient_refln.diffrn_id' diffrn_orient_refln yes '_diffrn_radiation.diffrn_id' diffrn_radiation yes '_diffrn_refln.diffrn_id' diffrn_refln yes '_diffrn_reflns.diffrn_id' diffrn_reflns yes '_diffrn_source.diffrn_id' diffrn_source yes '_diffrn_standard_refln.diffrn_id' diffrn_standard_refln yes '_diffrn_standards.diffrn_id' diffrn_standards yes loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_detector.diffrn_id' '_diffrn.id' '_diffrn_measurement.diffrn_id' '_diffrn.id' '_diffrn_orient_matrix.diffrn_id' '_diffrn.id' '_diffrn_orient_refln.diffrn_id' '_diffrn.id' '_diffrn_radiation.diffrn_id' '_diffrn.id' '_diffrn_refln.diffrn_id' '_diffrn.id' '_diffrn_reflns.diffrn_id' '_diffrn.id' '_diffrn_source.diffrn_id' '_diffrn.id' '_diffrn_standard_refln.diffrn_id' '_diffrn.id' '_diffrn_standards.diffrn_id' '_diffrn.id' _item_type.code code save_ ####################### ## DIFFRN_ATTENUATOR ## ####################### save_diffrn_attenuator _category.description ; Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. ; _category.id diffrn_attenuator _category.mandatory_code no _category_key.name '_diffrn_attenuator.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_attenuator.code 1 _diffrn_attenuator.scale 16.976 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_attenuator.code _item_description.description ; A code associated with a particular attenuator setting. This code is referenced by the _diffrn_refln.attenuator_code which is stored with the diffraction data. See _diffrn_attenuator.scale. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_attenuator.code' diffrn_attenuator yes _item_aliases.alias_name '_diffrn_attenuator_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.attenuator_code' '_diffrn_attenuator.code' _item_type.code code save_ save__diffrn_attenuator.scale _item_description.description ; The scale factor applied when an intensity measurement is reduced by an attenuator identified by _diffrn_attenuator.code. The measured intensity must be multiplied by this scale to convert it to the same scale as unattenuated intensities. ; _item.name '_diffrn_attenuator.scale' _item.category_id diffrn_attenuator _item.mandatory_code no _item_aliases.alias_name '_diffrn_attenuator_scale' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ ##################### ## DIFFRN_DETECTOR ## ##################### save_diffrn_detector _category.description ; Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. ; _category.id diffrn_detector _category.mandatory_code no _category_key.name '_diffrn_detector.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_detector.diffrn_id 'd1' _diffrn_detector.detector 'multiwire' _diffrn_detector.type 'Siemens' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_detector.details _item_description.description ; A description of special aspects of the radiation detector. ; _item.name '_diffrn_detector.details' _item.category_id diffrn_detector _item.mandatory_code no _item_aliases.alias_name '_diffrn_detector_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn_detector.detector _item_description.description ; The general class of the radiation detector. ; _item.name '_diffrn_detector.detector' _item.category_id diffrn_detector _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_radiation_detector' cifdic.c91 1.0 '_diffrn_detector' cif_core.dic 2.0 _item_type.code text loop_ _item_examples.case 'photographic film' 'scintillation counter' 'CCD plate' 'BF~3~ counter' save_ save__diffrn_detector.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_detector.diffrn_id' _item.mandatory_code yes save_ #save__diffrn_detector.dtime # _item_description.description #; The deadtime in microseconds of the detectors used to measure # the diffraction intensities. #; # _item.name '_diffrn_detector.dtime' # _item.category_id diffrn_detector # _item.mandatory_code no # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version '_diffrn_radiation_detector_dtime' # cifdic.c91 # 1.0 # '_diffrn_detector_dtime' # cif_core.dic # 2.0 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_type.code float # _item_units.code microseconds # save_ save__diffrn_detector.type _item_description.description ; The make, model or name of the detector device used. ; _item.name '_diffrn_detector.type' _item.category_id diffrn_detector _item.mandatory_code no _item_aliases.alias_name '_diffrn_detector_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ######################## ## DIFFRN_MEASUREMENT ## ######################## save_diffrn_measurement _category.description ; Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. ; _category.id diffrn_measurement _category.mandatory_code no _category_key.name '_diffrn_measurement.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_measurement.diffrn_id 'd1' _diffrn_measurement.device '3-circle camera' _diffrn_measurement.device_type 'Supper model x' _diffrn_measurement.device_details 'none' _diffrn_measurement.method 'omega scan' _diffrn_measurement.details ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_measurement.diffrn_id 's1' _diffrn_measurement.device_type 'Philips PW1100/20 diffractometer' _diffrn_measurement.method \q/2\q ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_measurement.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_measurement.diffrn_id' _item.mandatory_code yes save_ save__diffrn_measurement.details _item_description.description ; A description of special aspects of the intensity measurement. ; _item.name '_diffrn_measurement.details' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; save_ save__diffrn_measurement.device _item_description.description ; The general class of goniometer or device used to support and orient the specimen. ; _item.name '_diffrn_measurement.device' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case '3-circle camera' '4-circle camera' 'kappa-geometry camera' 'oscillation camera' 'precession camera' save_ save__diffrn_measurement.device_details _item_description.description ; A description of special aspects of the device used to measure the diffraction intensities. ; _item.name '_diffrn_measurement.device_details' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; commercial goniometer modified locally to allow for 90\% \t arc ; save_ save__diffrn_measurement.device_type _item_description.description ; The make, model or name of the measurement device (goniometer) used. ; _item.name '_diffrn_measurement.device_type' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Supper model q' 'Huber model r' 'Enraf-Nonius model s' 'homemade' save_ save__diffrn_measurement.method _item_description.description ; Method used to measure intensities. ; _item.name '_diffrn_measurement.method' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'profile data from theta/2theta scans' save_ save__diffrn_measurement.specimen_support _item_description.description ; The physical device used to support the crystal during data collection. ; _item.name '_diffrn_measurement.specimen_support' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_specimen_support' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'glass capillary' 'quartz capillary' 'fiber' 'metal loop' save_ ########################## ## DIFFRN_ORIENT_MATRIX ## ########################## save_diffrn_orient_matrix _category.description ; Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data. ; _category.id diffrn_orient_matrix _category.mandatory_code no _category_key.name '_diffrn_orient_matrix.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. ; ; _diffrn_orient_matrix.diffrn_id set1 _diffrn_orient_matrix.type ; reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles ; _diffrn_orient_matrix.UB[1][1] -0.071479 _diffrn_orient_matrix.UB[1][2] 0.020208 _diffrn_orient_matrix.UB[1][3] 0.039076 _diffrn_orient_matrix.UB[2][1] 0.035372 _diffrn_orient_matrix.UB[2][2] 0.056209 _diffrn_orient_matrix.UB[2][3] 0.078324 _diffrn_orient_matrix.UB[3][1] -0.007470 _diffrn_orient_matrix.UB[3][2] 0.067854 _diffrn_orient_matrix.UB[3][3] -0.017832 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_orient_matrix.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_orient_matrix.diffrn_id' _item.mandatory_code yes save_ save__diffrn_orient_matrix.type _item_description.description ; A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. ; _item.name '_diffrn_orient_matrix.type' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn_orient_matrix.UB[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[1][1]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__diffrn_orient_matrix.UB[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[1][2]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[1][3]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[2][1]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[2][2]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[2][3]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[3][1]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[3][2]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[3][3]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ ######################### ## DIFFRN_ORIENT_REFLN ## ######################### save_diffrn_orient_refln _category.description ; Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities. ; _category.id diffrn_orient_refln _category.mandatory_code no loop_ _category_key.name '_diffrn_orient_refln.diffrn_id' '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_k' '_diffrn_orient_refln.index_l' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. ; ; _diffrn_orient_refln.diffrn_id myset1 _diffrn_orient_refln.index_h 2 _diffrn_orient_refln.index_k 0 _diffrn_orient_refln.index_l 2 _diffrn_orient_refln.angle_chi -28.45 _diffrn_orient_refln.angle_kappa -11.32 _diffrn_orient_refln.angle_omega 5.33 _diffrn_orient_refln.angle_phi 101.78 _diffrn_orient_refln.angle_psi 0.00 _diffrn_orient_refln.angle_theta 10.66 # ... data abbreviated ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_orient_refln.angle_chi _item_description.description ; Diffractometer angle chi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_chi' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_chi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_kappa _item_description.description ; Diffractometer angle kappa of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_kappa' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_kappa' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_omega _item_description.description ; Diffractometer angle omega of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_omega' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_omega' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_phi _item_description.description ; Diffractometer angle phi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_phi' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_phi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_psi _item_description.description ; Diffractometer angle psi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_psi' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_psi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_theta _item_description.description ; Diffractometer angle theta of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_theta' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_theta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_orient_refln.diffrn_id' _item.mandatory_code yes save_ save__diffrn_orient_refln.index_h _item_description.description ; Miller index h of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_h' _item.category_id diffrn_orient_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_orient_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_k' '_diffrn_orient_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_orient_refln.index_k _item_description.description ; Miller index k of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_k' _item.category_id diffrn_orient_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_orient_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_orient_refln.index_l _item_description.description ; Miller index l of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_l' _item.category_id diffrn_orient_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_orient_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ ###################### ## DIFFRN_RADIATION ## ###################### save_diffrn_radiation _category.description ; Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. ; _category.id diffrn_radiation _category.mandatory_code no _category_key.name '_diffrn_radiation.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_radiation.diffrn_id 'set1' _diffrn_radiation.collimation '0.3 mm double pinhole' _diffrn_radiation.monochromator 'graphite' _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.wavelength_id 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_radiation.wavelength_id 1 _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.monochromator 'graphite' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_radiation.collimation _item_description.description ; The collimation or focusing applied to the radiation. ; _item.name '_diffrn_radiation.collimation' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_collimation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors' save_ save__diffrn_radiation.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_radiation.diffrn_id' _item.mandatory_code yes save_ save__diffrn_radiation.filter_edge _item_description.description ; Absorption edge in angstroms of the radiation filter used. ; _item.name '_diffrn_radiation.filter_edge' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_filter_edge' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__diffrn_radiation.inhomogeneity _item_description.description ; Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. ; _item.name '_diffrn_radiation.inhomogeneity' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_inhomogeneity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__diffrn_radiation.monochromator _item_description.description ; The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified. ; _item.name '_diffrn_radiation.monochromator' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_monochromator' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite' save_ save__diffrn_radiation.polarisn_norm _item_description.description ; The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See _diffrn_radiation.polarisn_ratio. ; _item.name '_diffrn_radiation.polarisn_norm' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_norm' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_radiation.polarisn_ratio _item_description.description ; Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel-polarized component of the radiation. The perpendicular component forms an angle of _diffrn_radiation.polarisn_norm to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). ; _item.name '_diffrn_radiation.polarisn_ratio' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_ratio' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__diffrn_radiation.probe _item_description.description ; The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information is given, so that the probe radiation can be simply determined. ; _item.name '_diffrn_radiation.probe' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_probe' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value 'x-ray' 'neutron' 'electron' 'gamma' save_ save__diffrn_radiation.type _item_description.description ; The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. ; _item.name '_diffrn_radiation.type' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'CuK\a' 'Cu K\a~1~' 'Cu K-L~2,3~' 'white-beam' save_ save__diffrn_radiation.xray_symbol _item_description.description ; The IUPAC symbol for the X-ray wavelength for the probe radiation. ; _item.name '_diffrn_radiation.xray_symbol' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_xray_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'K-L~3~' 'K\a~1~ in older Siegbahn notation' 'K-L~2~' 'K\a~2~ in older Siegbahn notation' 'K-M~3~' 'K\b~1~ in older Siegbahn notation' 'K-L~2,3~' 'use where K-L~3~ and K-L~2~ are not resolved' save_ save__diffrn_radiation.wavelength_id _item_description.description ; This data item is a pointer to _diffrn_radiation_wavelength.id in the DIFFRN_RADIATION_WAVELENGTH category. ; _item.name '_diffrn_radiation.wavelength_id' _item.mandatory_code yes save_ ################################# ## DIFFRN_RADIATION_WAVELENGTH ## ################################# save_diffrn_radiation_wavelength _category.description ; Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam. ; _category.id diffrn_radiation_wavelength _category.mandatory_code no _category_key.name '_diffrn_radiation_wavelength.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_radiation_wavelength.id _item_description.description ; The code identifying each value of _diffrn_radiation_wavelength.wavelength. Items in the DIFFRN_RADIATION_WAVELENGTH category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN category. The _diffrn_refln.wavelength_id codes must match one of the codes defined in this category. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_radiation_wavelength.id' diffrn_radiation_wavelength yes '_diffrn_radiation.wavelength_id' diffrn_radiation yes '_diffrn_refln.wavelength_id' diffrn_refln yes '_refln.wavelength_id' refln yes _item_aliases.alias_name '_diffrn_radiation_wavelength_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_radiation.wavelength_id' '_diffrn_radiation_wavelength.id' '_diffrn_refln.wavelength_id' '_diffrn_radiation_wavelength.id' '_refln.wavelength_id' '_diffrn_radiation_wavelength.id' _item_type.code code loop_ _item_examples.case 'x1' 'x2' 'neut' save_ save__diffrn_radiation_wavelength.wavelength _item_description.description ; The radiation wavelength in angstroms. ; _item.name '_diffrn_radiation_wavelength.wavelength' _item.category_id diffrn_radiation_wavelength _item.mandatory_code yes _item_aliases.alias_name '_diffrn_radiation_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__diffrn_radiation_wavelength.wt _item_description.description ; The relative weight of a wavelength identified by the code _diffrn_radiation_wavelength.id in the list of wavelengths. ; _item.name '_diffrn_radiation_wavelength.wt' _item.category_id diffrn_radiation_wavelength _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_wavelength_wt' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ ################## ## DIFFRN_REFLN ## ################## save_diffrn_refln _category.description ; Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by _diffrn_refln.diffrn_id. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by _diffrn_reflns.diffrn_id. ; _category.id diffrn_refln _category.mandatory_code no loop_ _category_key.name '_diffrn_refln.diffrn_id' '_diffrn_refln.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102. ; ; _diffrn_refln.diffrn_id set1 _diffrn_refln.id 1102 _diffrn_refln.wavelength_id Cu1fixed _diffrn_refln.angle_chi 32.21 _diffrn_refln.angle_kappa 20.12 _diffrn_refln.angle_omega 11.54 _diffrn_refln.angle_phi 176.02 _diffrn_refln.angle_psi 0.00 _diffrn_refln.angle_theta 23.08 _diffrn_refln.attenuator_code 'Ni.005' _diffrn_refln.counts_bg_1 22 _diffrn_refln.counts_bg_2 25 _diffrn_refln.counts_net 3450 _diffrn_refln.counts_peak 321 _diffrn_refln.counts_total 3499 _diffrn_refln.detect_slit_horiz 0.04 _diffrn_refln.detect_slit_vert 0.02 _diffrn_refln.elapsed_time 1.00 _diffrn_refln.index_h 4 _diffrn_refln.index_k 0 _diffrn_refln.index_l 2 _diffrn_refln.intensity_net 202.56 _diffrn_refln.intensity_sigma 2.18 _diffrn_refln.scale_group_code A24 _diffrn_refln.scan_mode om _diffrn_refln.scan_mode_backgd mo _diffrn_refln.scan_rate 1.2 _diffrn_refln.scan_time_backgd 900.00 _diffrn_refln.scan_width 1.0 _diffrn_refln.sint_over_lambda 0.25426 _diffrn_refln.standard_code 1 _diffrn_refln.wavelength 1.54184 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_refln.angle_chi _item_description.description ; The diffractometer angle chi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_chi' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_chi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_kappa _item_description.description ; The diffractometer angle kappa of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_kappa' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_kappa' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_omega _item_description.description ; The diffractometer angle omega of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_omega' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_omega' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_phi _item_description.description ; The diffractometer angle phi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_phi' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_phi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_psi _item_description.description ; The diffractometer angle psi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_psi' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_psi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_theta _item_description.description ; The diffractometer angle theta of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_theta' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_theta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.attenuator_code _item_description.description ; The code identifying the attenuator setting for this reflection. This code must match one of the _diffrn_attenuator.code values. ; _item.name '_diffrn_refln.attenuator_code' _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_attenuator_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn_refln.counts_bg_1 _item_description.description ; The diffractometer counts for the measurement of the background before the peak. ; _item.name '_diffrn_refln.counts_bg_1' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_bg_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_bg_2 _item_description.description ; The diffractometer counts for the measurement of the background after the peak. ; _item.name '_diffrn_refln.counts_bg_2' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_bg_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_net _item_description.description ; The diffractometer counts for the measurement of net counts after background removal. ; _item.name '_diffrn_refln.counts_net' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_net' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_peak _item_description.description ; The diffractometer counts for the measurement of counts for the peak scan or position. ; _item.name '_diffrn_refln.counts_peak' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_peak' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_total _item_description.description ; The diffractometer counts for the measurement of total counts (background plus peak). ; _item.name '_diffrn_refln.counts_total' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_total' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.detect_slit_horiz _item_description.description ; Total slit aperture in degrees in the diffraction plane. ; _item.name '_diffrn_refln.detect_slit_horiz' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_horiz' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.detect_slit_vert _item_description.description ; Total slit aperture in degrees perpendicular to the diffraction plane. ; _item.name '_diffrn_refln.detect_slit_vert' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_vert' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_refln.diffrn_id' _item.mandatory_code yes save_ save__diffrn_refln.elapsed_time _item_description.description ; Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity. ; _item.name '_diffrn_refln.elapsed_time' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_elapsed_time' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code minutes save_ save__diffrn_refln.id _item_description.description ; The value of _diffrn_refln.id must uniquely identify the reflection in the data set identified by the item _diffrn_refln.diffrn_id. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_diffrn_refln.id' _item.category_id diffrn_refln _item.mandatory_code yes _item_type.code code save_ save__diffrn_refln.index_h _item_description.description ; Miller index h of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][]. ; _item.name '_diffrn_refln.index_h' _item.category_id diffrn_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_refln.index_k _item_description.description ; Miller index k of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][]. ; _item.name '_diffrn_refln.index_k' _item.category_id diffrn_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_refln.index_l _item_description.description ; Miller index l of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][]. ; _item.name '_diffrn_refln.index_l' _item.category_id diffrn_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_refln.intensity_net _item_description.description ; Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_net' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_intensity_net' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code float save_ save__diffrn_refln.intensity_sigma _item_description.description ; Standard uncertainty (estimated standard deviation) of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_sigma' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_intensity_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code float save_ save__diffrn_refln.scale_group_code _item_description.description ; The code identifying the scale applying to this reflection. This data item is a pointer to _diffrn_scale_group.code in the DIFFRN_SCALE_GROUP category. ; _item.name '_diffrn_refln.scale_group_code' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn_refln.scan_mode _item_description.description ; The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. ; _item.name '_diffrn_refln.scan_mode' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_mode' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail om 'omega scan' ot 'omega/2theta scan' q 'Q scans (arbitrary reciprocal directions)' save_ save__diffrn_refln.scan_mode_backgd _item_description.description ; The code identifying the mode of scanning a reflection to measure the background intensity. ; _item.name '_diffrn_refln.scan_mode_backgd' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_mode_backgd' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail st 'stationary counter background' mo 'moving counter background' save_ save__diffrn_refln.scan_rate _item_description.description ; The rate of scanning a reflection in degrees per minute to measure the intensity. ; _item.name '_diffrn_refln.scan_rate' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_rate' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees_per_minute save_ save__diffrn_refln.scan_time_backgd _item_description.description ; The time spent measuring each background in seconds. ; _item.name '_diffrn_refln.scan_time_backgd' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_time_backgd' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code seconds save_ save__diffrn_refln.scan_width _item_description.description ; The scan width in degrees of the scan mode defined by the code _diffrn_refln.scan_mode. ; _item.name '_diffrn_refln.scan_width' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_width' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.sint_over_lambda _item_description.description ; The (sin theta)/lambda value in reciprocal angstroms for this reflection. ; _item.name '_diffrn_refln.sint_over_lambda' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_sint/lambda' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code reciprocal_angstroms save_ save__diffrn_refln.standard_code _item_description.description ; The code identifying that this reflection was measured as a standard intensity. This data item is a pointer to _diffrn_standard_refln.code in the DIFFRN_STANDARD_REFLN category. ; _item.name '_diffrn_refln.standard_code' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_standard_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn_refln.wavelength _item_description.description ; The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. ; _item.name '_diffrn_refln.wavelength' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__diffrn_refln.wavelength_id _item_description.description ; This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category. ; _item.name '_diffrn_refln.wavelength_id' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_wavelength_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ ################### ## DIFFRN_REFLNS ## ################### save_diffrn_reflns _category.description ; Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set. ; _category.id diffrn_reflns _category.mandatory_code no _category_key.name '_diffrn_reflns.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' # loop_ # _category_examples.detail # _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_reflns.av_R_equivalents _item_description.description ; The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average absolute difference between av(I) and the individual symmetry-equivalent intensities. ; _item.name '_diffrn_reflns.av_R_equivalents' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_av_R_equivalents' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__diffrn_reflns.av_sigmaI_over_netI _item_description.description ; Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. ; _item.name '_diffrn_reflns.av_sigmaI_over_netI' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_av_sigmaI/netI' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__diffrn_reflns.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_reflns.diffrn_id' _item.mandatory_code yes save_ save__diffrn_reflns.limit_h_max _item_description.description ; The maximum value of the Miller index h for the reflection data specified by _diffrn_refln.index_h. ; _item.name '_diffrn_reflns.limit_h_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_h_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_h_min _item_description.description ; The minimum value of the Miller index h for the reflection data specified by _diffrn_refln.index_h. ; _item.name '_diffrn_reflns.limit_h_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_h_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_k_max _item_description.description ; The maximum value of the Miller index k for the reflection data specified by _diffrn_refln.index_k. ; _item.name '_diffrn_reflns.limit_k_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_k_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_k_min _item_description.description ; The minimum value of the Miller index k for the reflection data specified by _diffrn_refln.index_k. ; _item.name '_diffrn_reflns.limit_k_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_k_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_l_max _item_description.description ; The maximum value of the Miller index l for the reflection data specified by _diffrn_refln.index_l. ; _item.name '_diffrn_reflns.limit_l_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_l_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_l_min _item_description.description ; The minimum value of the Miller index l for the reflection data specified by _diffrn_refln.index_l. ; _item.name '_diffrn_reflns.limit_l_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_l_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.number _item_description.description ; The total number of measured intensities, excluding reflections that are classified as systematically absent. ; _item.name '_diffrn_reflns.number' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_reflns.reduction_process _item_description.description ; A description of the process used to reduce the intensity data into structure-factor magnitudes. ; _item.name '_diffrn_reflns.reduction_process' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_reduction_process' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'data averaged using Fisher test' save_ save__diffrn_reflns.theta_max _item_description.description ; Maximum theta angle in degrees for the measured diffraction intensities. ; _item.name '_diffrn_reflns.theta_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_reflns.theta_min _item_description.description ; Minimum theta angle in degrees for the measured diffraction intensities. ; _item.name '_diffrn_reflns.theta_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_reflns.transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[1][1]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[1][2]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[1][3]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[2][1]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[2][2]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[2][3]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[3][1]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[3][2]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[3][3]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ ######################## ## DIFFRN_SCALE_GROUP ## ######################## save_diffrn_scale_group _category.description ; Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set. ; _category.id diffrn_scale_group _category.mandatory_code no _category_key.name '_diffrn_scale_group.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. ; ; _diffrn_scale_group.code A24 _diffrn_scale_group.I_net 1.021 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_scale_group.code _item_description.description ; The value of _diffrn_scale_group.code must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_scale_group.code' diffrn_scale_group yes '_diffrn_refln.scale_group_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.scale_group_code' '_diffrn_scale_group.code' _item_type.code code loop_ _item_examples.case '1' '2' 'c1' 'c2' save_ save__diffrn_scale_group.I_net _item_description.description ; The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the DIFFRN_REFLN or REFLN list on a common scale. ; _item.name '_diffrn_scale_group.I_net' _item.category_id diffrn_scale_group _item.mandatory_code no _item_aliases.alias_name '_diffrn_scale_group_I_net' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################### ## DIFFRN_SOURCE ## ################### save_diffrn_source _category.description ; Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment. ; _category.id diffrn_source _category.mandatory_code no _category_key.name '_diffrn_source.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_source.diffrn_id 's1' _diffrn_source.source 'rotating anode' _diffrn_source.type 'Rigaku RU-200' _diffrn_source.power 50 _diffrn_source.current 180 _diffrn_source.size '8mm x 0.4 mm broad-focus' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_source.current _item_description.description ; The current in milliamperes at which the radiation source was operated. ; _item.name '_diffrn_source.current' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_current' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code milliamperes save_ save__diffrn_source.details _item_description.description ; A description of special aspects of the radiation source used. ; _item.name '_diffrn_source.details' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn_source.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_source.diffrn_id' _item.mandatory_code yes save_ save__diffrn_source.power _item_description.description ; The power in kilowatts at which the radiation source was operated. ; _item.name '_diffrn_source.power' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_power' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code kilowatts save_ save__diffrn_source.size _item_description.description ; The dimensions of the source as viewed from the sample. ; _item.name '_diffrn_source.size' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_size' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case '8mm x 0.4 mm fine-focus' 'broad focus' save_ save__diffrn_source.source _item_description.description ; The general class of the radiation source. ; _item.name '_diffrn_source.source' _item.category_id diffrn_source _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_radiation_source' cifdic.c91 1.0 '_diffrn_source' cif_core.dic 2.0 _item_type.code text loop_ _item_examples.case 'sealed X-ray tube' 'nuclear reactor' 'spallation source' 'electron microscope' 'rotating-anode X-ray tube' 'synchrotron' save_ save__diffrn_source.target _item_description.description ; The chemical element symbol for the X-ray target (usually the anode) used to generate X-rays. This can also be used for spallation sources. ; _item.name '_diffrn_source.target' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_target' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_enumeration.value H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr save_ save__diffrn_source.type _item_description.description ; The make, model or name of the source of radiation. ; _item.name '_diffrn_source.type' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'NSLS beamline X8C' 'Rigaku RU200' save_ save__diffrn_source.voltage _item_description.description ; The voltage in kilovolts at which the radiation source was operated. ; _item.name '_diffrn_source.voltage' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_voltage' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code kilovolts save_ ########################### ## DIFFRN_STANDARD_REFLN ## ########################### save_diffrn_standard_refln _category.description ; Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. ; _category.id diffrn_standard_refln _category.mandatory_code no loop_ _category_key.name '_diffrn_standard_refln.diffrn_id' '_diffrn_standard_refln.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _diffrn_standard_refln.diffrn_id _diffrn_standard_refln.code _diffrn_standard_refln.index_h _diffrn_standard_refln.index_k _diffrn_standard_refln.index_l s1 1 3 2 4 s1 1 1 9 1 s1 1 3 0 10 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_standard_refln.code _item_description.description ; The code identifying a reflection measured as a standard reflection with the indices _diffrn_standard_refln.index_h, _diffrn_standard_refln.index_k and _diffrn_standard_refln.index_l. This is the same code as the _diffrn_refln.standard_code in the DIFFRN_REFLN list. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_standard_refln.code' diffrn_standard_refln yes '_diffrn_refln.standard_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_standard_refln_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.standard_code' '_diffrn_standard_refln.code' _item_type.code code loop_ _item_examples.case '1' '2' 'c1' 'c2' save_ save__diffrn_standard_refln.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_standard_refln.diffrn_id' _item.mandatory_code yes save_ save__diffrn_standard_refln.index_h _item_description.description ; Miller index h of a standard reflection used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_h' _item.category_id diffrn_standard_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_standard_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_k' '_diffrn_standard_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_standard_refln.index_k _item_description.description ; Miller index k of a standard reflection used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_k' _item.category_id diffrn_standard_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_standard_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_h' '_diffrn_standard_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_standard_refln.index_l _item_description.description ; Miller index l of a standard reflection used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_l' _item.category_id diffrn_standard_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_standard_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_h' '_diffrn_standard_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ ###################### ## DIFFRN_STANDARDS ## ###################### save_diffrn_standards _category.description ; Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. ; _category.id diffrn_standards _category.mandatory_code no _category_key.name '_diffrn_standards.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_standards.diffrn_id 's1' _diffrn_standards.number 3 _diffrn_standards.interval_time 120 _diffrn_standards.decay_% 0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_standards.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_standards.diffrn_id' _item.mandatory_code yes save_ save__diffrn_standards.decay_% _item_description.description ; The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones. ; _item.name '_diffrn_standards.decay_%' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_decay_%' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 100.0 100.0 100.0 . _item_type.code float save_ save__diffrn_standards.interval_count _item_description.description ; The number of reflection intensities between the measurement of standard reflection intensities. ; _item.name '_diffrn_standards.interval_count' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_interval_count' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_standards.interval_time _item_description.description ; The time in minutes between the measurement of standard reflection intensities. ; _item.name '_diffrn_standards.interval_time' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_interval_time' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code float _item_units.code minutes save_ save__diffrn_standards.number _item_description.description ; The number of unique standard reflections used during the measurement of the diffraction intensities. ; _item.name '_diffrn_standards.number' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_standards.scale_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of the individual mean standard scales applied to the intensity data. ; _item.name '_diffrn_standards.scale_sigma' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_scale_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ############ ## ENTITY ## ############ save_entity _category.description ; Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. ; _category.id entity _category.mandatory_code no _category_key.name '_entity.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity.id _entity.type _entity.formula_weight _entity.details 1 polymer 10916 ; The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer. ; 2 non-polymer '762' . 3 water 18 . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity.details _item_description.description ; A description of special aspects of the entity. ; _item.name '_entity.details' _item.category_id entity _item.mandatory_code no _item_type.code text save_ save__entity.formula_weight _item_description.description ; Formula mass in daltons of the entity. ; _item.name '_entity.formula_weight' _item.category_id entity _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__entity.id _item_description.description ; The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity.id' entity yes '_atom_site.label_entity_id' atom_site no '_entity_keywords.entity_id' entity_keywords yes '_entity_link.entity_id_1' entity_link yes '_entity_link.entity_id_2' entity_link yes '_entity_name_com.entity_id' entity_name_com yes '_entity_name_sys.entity_id' entity_name_sys yes '_entity_poly.entity_id' entity_poly yes '_entity_poly_seq.entity_id' entity_poly_seq yes '_entity_src_gen.entity_id' entity_src_gen yes '_entity_src_nat.entity_id' entity_src_nat yes '_struct_asym.entity_id' struct_asym yes '_struct_ref.entity_id' struct_ref yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_entity_id' '_entity.id' '_entity_keywords.entity_id' '_entity.id' '_entity_link.entity_id_1' '_entity.id' '_entity_link.entity_id_2' '_entity.id' '_entity_name_com.entity_id' '_entity.id' '_entity_name_sys.entity_id' '_entity.id' '_entity_poly.entity_id' '_entity.id' '_entity_poly_seq.entity_id' '_entity_poly.entity_id' '_entity_src_gen.entity_id' '_entity.id' '_entity_src_nat.entity_id' '_entity.id' '_struct_asym.entity_id' '_entity.id' '_struct_ref.entity_id' '_entity.id' save_ save__entity.src_method _item_description.description ; The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. ; _item.name '_entity.src_method' _item.category_id entity _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail nat ; entity isolated from a natural source ; man ; entity isolated from a genetically manipulated source ; syn ; entity obtained synthetically ; save_ save__entity.type _item_description.description ; Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. ; _item.name '_entity.type' _item.category_id entity _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail polymer 'entity is a polymer' non-polymer 'entity is not a polymer' water 'water in the solvent model' save_ ##################### ## ENTITY_KEYWORDS ## ##################### save_entity_keywords _category.description ; Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA. ; _category.id entity_keywords _category.mandatory_code no _category_key.name '_entity_keywords.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_keywords.entity_id _entity_keywords.text 2 'natural product, inhibitor, reduced peptide' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_keywords.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_keywords.entity_id' _item.mandatory_code yes save_ save__entity_keywords.text _item_description.description ; Keywords describing this entity. ; _item.name '_entity_keywords.text' _item.category_id entity_keywords _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'polypeptide' 'natural product' 'polysaccharide' save_ ################# ## ENTITY_LINK ## ################# save_entity_link _category.description ; Data items in the ENTITY_LINK category give details about the links between entities. ; _category.id entity_link _category.mandatory_code no _category_key.name '_entity_link.link_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__entity_link.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_entity_link.link_id' _item.mandatory_code yes save_ save__entity_link.details _item_description.description ; A description of special aspects of a link between chemical components in the structure. ; _item.name '_entity_link.details' _item.category_id entity_link _item.mandatory_code no _item_type.code text save_ save__entity_link.entity_id_1 _item_description.description ; The entity ID of the first of the two entities joined by the link. This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_link.entity_id_1' _item.mandatory_code yes save_ save__entity_link.entity_id_2 _item_description.description ; The entity ID of the second of the two entities joined by the link. This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_link.entity_id_2' _item.mandatory_code yes save_ save__entity_link.entity_seq_num_1 _item_description.description ; For a polymer entity, the sequence number in the first of the two entities containing the link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_entity_link.entity_seq_num_1' _item.mandatory_code no save_ save__entity_link.entity_seq_num_2 _item_description.description ; For a polymer entity, the sequence number in the second of the two entities containing the link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_entity_link.entity_seq_num_2' _item.mandatory_code no save_ ##################### ## ENTITY_NAME_COM ## ##################### save_entity_name_com _category.description ; Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin. ; _category.id entity_name_com _category.mandatory_code no loop_ _category_key.name '_entity_name_com.entity_id' '_entity_name_com.name' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_name_com.entity_id _entity_name_com.name 1 'HIV-1 protease monomer' 1 'HIV-1 PR monomer' 2 'acetyl-pepstatin' 2 'acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine' 3 'water' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_name_com.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_name_com.entity_id' _item.mandatory_code yes save_ save__entity_name_com.name _item_description.description ; A common name for the entity. ; _item.name '_entity_name_com.name' _item.category_id entity_name_com _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'HIV protease monomer' 'hemoglobin alpha chain' '2-fluoro-1,4-dichloro benzene' 'arbutin' save_ ##################### ## ENTITY_NAME_SYS ## ##################### save_entity_name_sys _category.description ; Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. ; _category.id entity_name_sys _category.mandatory_code no loop_ _category_key.name '_entity_name_sys.entity_id' '_entity_name_sys.name' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_name_sys.entity_id _entity_name_sys.name 1 'EC 3.4.23.16' 2 'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta' 3 water ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_name_sys.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_name_sys.entity_id' _item.mandatory_code yes save_ save__entity_name_sys.name _item_description.description ; The systematic name for the entity. ; _item.name '_entity_name_sys.name' _item.category_id entity_name_sys _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'hydroquinone-beta-D-pyranoside' 'EC 2.1.1.1' '2-fluoro-1,4-dichlorobenzene' save_ save__entity_name_sys.system _item_description.description ; The system used to generate the systematic name of the entity. ; _item.name '_entity_name_sys.system' _item.category_id entity_name_sys _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Chemical Abstracts conventions' 'enzyme convention' 'Sigma catalog' save_ ################# ## ENTITY_POLY ## ################# save_entity_poly _category.description ; Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. ; _category.id entity_poly _category.mandatory_code no _category_key.name '_entity_poly.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_chirality _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.type_details 1 polypeptide(L) no no no . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_poly.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_poly.entity_id' _item.mandatory_code yes save_ save__entity_poly.nstd_chirality _item_description.description ; A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in _entity_poly.type. ; _item.name '_entity_poly.nstd_chirality' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no ; polymer contains no monomers with different chirality ; n ; abbreviation for "no" ; yes ; polymer contains at least one monomer with different chirality ; y ; abbreviation for "yes" ; save_ save__entity_poly.nstd_linkage _item_description.description ; A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by _entity_poly.type. ; _item.name '_entity_poly.nstd_linkage' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'polymer contains no different links' n 'abbreviation for "no"' yes ; polymer contains at least one different link ; y 'abbreviation for "yes"' save_ save__entity_poly.nstd_monomer _item_description.description ; A flag to indicate whether the polymer contains at least one monomer that is not considered standard. ; _item.name '_entity_poly.nstd_monomer' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'polymer contains no nonstandard monomers' n 'abbreviation for "no"' yes ; polymer contains at least one nonstandard monomer ; y 'abbreviation for "yes"' save_ save__entity_poly.number_of_monomers _item_description.description ; The number of monomers in the polymer. ; _item.name '_entity_poly.number_of_monomers' _item.category_id entity_poly _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__entity_poly.type _item_description.description ; The type of the polymer. ; _item.name '_entity_poly.type' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value 'polypeptide(D)' 'polypeptide(L)' 'polydeoxyribonucleotide' 'polyribonucleotide' 'polysaccharide(D)' 'polysaccharide(L)' 'other' save_ save__entity_poly.type_details _item_description.description ; A description of special aspects of the polymer type. ; _item.name '_entity_poly.type_details' _item.category_id entity_poly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'monomer Ala 16 is a D-amino acid' 'the oligomer contains alternating RNA and DNA units' save_ ##################### ## ENTITY_POLY_SEQ ## ##################### save_entity_poly_seq _category.description ; Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. ; _category.id entity_poly_seq _category.mandatory_code no loop_ _category_key.name '_entity_poly_seq.entity_id' '_entity_poly_seq.num' '_entity_poly_seq.mon_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 PRO 1 2 GLN 1 3 ILE 1 4 THR 1 5 LEU 1 6 TRP 1 7 GLN 1 8 ARG 1 9 PRO 1 10 LEU 1 11 VAL 1 12 THR 1 13 ILE 1 14 LYS 1 15 ILE 1 16 GLY 1 17 GLY 1 18 GLN 1 19 LEU 1 20 LYS 1 21 GLU 1 22 ALA 1 23 LEU 1 24 LEU 1 25 ASP # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_poly_seq.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_poly_seq.entity_id' _item.mandatory_code yes save_ save__entity_poly_seq.hetero _item_description.description ; A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. This would be rare. ; _item.name '_entity_poly_seq.hetero' _item.category_id entity_poly_seq _item.mandatory_code no _item_default.value no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'sequence is not heterogeneous at this monomer' n 'abbreviation for "no"' yes 'sequence is heterogeneous at this monomer' y 'abbreviation for "yes"' save_ save__entity_poly_seq.mon_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_entity_poly_seq.mon_id' _item.mandatory_code yes save_ save__entity_poly_seq.num _item_description.description ; The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_poly_seq.num' entity_poly_seq yes '_atom_site.label_seq_id' atom_site no '_entity_link.entity_seq_num_1' entity_link no '_entity_link.entity_seq_num_2' entity_link no '_geom_angle.atom_site_label_seq_id_1' geom_angle no '_geom_angle.atom_site_label_seq_id_2' geom_angle no '_geom_angle.atom_site_label_seq_id_3' geom_angle no '_geom_bond.atom_site_label_seq_id_1' geom_bond no '_geom_bond.atom_site_label_seq_id_2' geom_bond no '_geom_contact.atom_site_label_seq_id_1' geom_contact no '_geom_contact.atom_site_label_seq_id_2' geom_contact no '_geom_hbond.atom_site_label_seq_id_A' geom_hbond no '_geom_hbond.atom_site_label_seq_id_D' geom_hbond no '_geom_hbond.atom_site_label_seq_id_H' geom_hbond no '_geom_torsion.atom_site_label_seq_id_1' geom_torsion no '_geom_torsion.atom_site_label_seq_id_2' geom_torsion no '_geom_torsion.atom_site_label_seq_id_3' geom_torsion no '_geom_torsion.atom_site_label_seq_id_4' geom_torsion no '_struct_conf.beg_label_seq_id' struct_conf yes '_struct_conf.end_label_seq_id' struct_conf yes '_struct_conn.ptnr1_label_seq_id' struct_conn yes '_struct_conn.ptnr2_label_seq_id' struct_conn yes '_struct_mon_nucl.label_seq_id' struct_mon_nucl yes '_struct_mon_prot.label_seq_id' struct_mon_prot yes '_struct_mon_prot_cis.label_seq_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_seq_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_seq_id' struct_ncs_dom_lim yes '_struct_ref_seq.seq_align_beg' struct_ref_seq yes '_struct_ref_seq.seq_align_end' struct_ref_seq yes '_struct_ref_seq_dif.seq_num' struct_ref_seq_dif yes '_struct_sheet_hbond.range_1_beg_label_seq_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_1_end_label_seq_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_beg_label_seq_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_end_label_seq_id' struct_sheet_hbond yes '_struct_sheet_range.beg_label_seq_id' struct_sheet_range yes '_struct_sheet_range.end_label_seq_id' struct_sheet_range yes '_struct_site_gen.label_seq_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_seq_id' '_entity_poly_seq.num' '_entity_link.entity_seq_num_1' '_entity_poly_seq.num' '_entity_link.entity_seq_num_2' '_entity_poly_seq.num' '_geom_angle.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_angle.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_angle.atom_site_label_seq_id_3' '_atom_site.label_seq_id' '_geom_bond.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_bond.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_contact.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_contact.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_hbond.atom_site_label_seq_id_A' '_atom_site.label_seq_id' '_geom_hbond.atom_site_label_seq_id_D' '_atom_site.label_seq_id' '_geom_hbond.atom_site_label_seq_id_H' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_3' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_4' '_atom_site.label_seq_id' '_struct_conf.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_conf.end_label_seq_id' '_atom_site.label_seq_id' '_struct_conn.ptnr1_label_seq_id' '_atom_site.label_seq_id' '_struct_conn.ptnr2_label_seq_id' '_atom_site.label_seq_id' '_struct_mon_nucl.label_seq_id' '_atom_site.label_seq_id' '_struct_mon_prot.label_seq_id' '_atom_site.label_seq_id' '_struct_mon_prot_cis.label_seq_id' '_atom_site.label_seq_id' '_struct_ncs_dom_lim.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_ncs_dom_lim.end_label_seq_id' '_atom_site.label_seq_id' '_struct_ref_seq.seq_align_beg' '_entity_poly_seq.num' '_struct_ref_seq.seq_align_end' '_entity_poly_seq.num' '_struct_ref_seq_dif.seq_num' '_entity_poly_seq.num' '_struct_sheet_hbond.range_1_beg_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_hbond.range_1_end_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_hbond.range_2_beg_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_hbond.range_2_end_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_range.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_range.end_label_seq_id' '_atom_site.label_seq_id' '_struct_site_gen.label_seq_id' '_atom_site.label_seq_id' loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ #################### ## ENTITY_SRC_GEN ## #################### save_entity_src_gen _category.description ; Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). ; _category.id entity_src_gen _category.mandatory_code no _category_key.name '_entity_src_gen.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_src_gen.entity_id _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.host_org_common_name _entity_src_gen.host_org_genus _entity_src_gen.host_org_species _entity_src_gen.plasmid_name 1 'HIV-1' '?' '?' 'NY-5' 'bacteria' 'Escherichia' 'coli' 'pB322' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_src_gen.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_src_gen.entity_id' _item.mandatory_code yes save_ save__entity_src_gen.gene_src_common_name _item_description.description ; The common name of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_common_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'man' 'yeast' 'bacteria' save_ save__entity_src_gen.gene_src_details _item_description.description ; A description of special aspects of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.gene_src_genus _item_description.description ; The genus of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_genus' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Homo' 'Saccharomyces' 'Escherichia' save_ save__entity_src_gen.gene_src_species _item_description.description ; The species of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_species' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'sapiens' 'cerevisiae' 'coli' save_ save__entity_src_gen.gene_src_strain _item_description.description ; The strain of the natural organism from which the gene was obtained, if relevant. ; _item.name '_entity_src_gen.gene_src_strain' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__entity_src_gen.gene_src_tissue _item_description.description ; The tissue of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_tissue' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' save_ save__entity_src_gen.gene_src_tissue_fraction _item_description.description ; The subcellular fraction of the tissue of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_tissue_fraction' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'mitochondria' 'nucleus' 'membrane' save_ save__entity_src_gen.host_org_common_name _item_description.description ; The common name of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_common_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'yeast' 'bacteria' save_ save__entity_src_gen.host_org_details _item_description.description ; A description of special aspects of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.host_org_genus _item_description.description ; The genus of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_genus' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Saccharomyces' 'Escherichia' save_ save__entity_src_gen.host_org_species _item_description.description ; The species of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_species' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'cerevisiae' 'coli' save_ save__entity_src_gen.host_org_strain _item_description.description ; The strain of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_strain' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__entity_src_gen.plasmid_details _item_description.description ; A description of special aspects of the plasmid that produced the entity in the host organism. ; _item.name '_entity_src_gen.plasmid_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.plasmid_name _item_description.description ; The name of the plasmid that produced the entity in the host organism. ; _item.name '_entity_src_gen.plasmid_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'pET3C' 'pT123sab' save_ #################### ## ENTITY_SRC_NAT ## #################### save_entity_src_nat _category.description ; Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue. ; _category.id entity_src_nat _category.mandatory_code no _category_key.name '_entity_src_nat.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_src_nat.entity_id _entity_src_nat.common_name _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.details 2 'bacteria' 'Actinomycetes' '?' ; Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture University, and provided to us by Dr. Ben Dunn, University of Florida, and Dr. J. Kay, University of Wales. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_src_nat.common_name _item_description.description ; The common name of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.common_name' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'man' 'yeast' 'bacteria' save_ save__entity_src_nat.details _item_description.description ; A description of special aspects of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.details' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text save_ save__entity_src_nat.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_src_nat.entity_id' _item.mandatory_code yes save_ save__entity_src_nat.genus _item_description.description ; The genus of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.genus' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'Homo' 'Saccharomyces' 'Escherichia' save_ save__entity_src_nat.species _item_description.description ; The species of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.species' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'sapiens' 'cerevisiae' 'coli' save_ save__entity_src_nat.strain _item_description.description ; The strain of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.strain' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__entity_src_nat.tissue _item_description.description ; The tissue of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.tissue' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' save_ save__entity_src_nat.tissue_fraction _item_description.description ; The subcellular fraction of the tissue of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.tissue_fraction' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'mitochondria' 'nucleus' 'membrane' save_ ########### ## ENTRY ## ########### save_entry _category.description ; There is only one item in the ENTRY category, _entry.id. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. ; _category.id entry _category.mandatory_code no _category_key.name '_entry.id' loop_ _category_group.id 'inclusive_group' 'entry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _entry.id '5HVP' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _entry.id 'TOZ' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entry.id _item_description.description ; The value of _entry.id identifies the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entry.id' entry yes '_atom_sites.entry_id' atom_sites yes '_cell.entry_id' cell yes '_cell_measurement.entry_id' cell_measurement yes '_chemical.entry_id' chemical yes '_chemical_formula.entry_id' chemical_formula yes '_computing.entry_id' computing yes '_database.entry_id' database yes '_database_PDB_matrix.entry_id' database_PDB_matrix yes '_entry_link.entry_id' entry_link yes '_exptl.entry_id' exptl yes '_geom.entry_id' geom yes '_journal.entry_id' journal yes '_phasing_averaging.entry_id' phasing_averaging yes '_phasing_isomorphous.entry_id' phasing_isomorphous yes '_phasing_MAD.entry_id' phasing_MAD yes '_phasing_MIR.entry_id' phasing_MIR yes '_publ.entry_id' publ yes '_publ_manuscript_incl.entry_id' publ_manuscript_incl yes '_refine.entry_id' refine yes '_refine_analyze.entry_id' refine_analyze yes '_reflns.entry_id' reflns yes '_struct.entry_id' struct yes '_struct_keywords.entry_id' struct_keywords yes '_struct_mon_details.entry_id' struct_mon_details yes '_symmetry.entry_id' symmetry yes _item_aliases.alias_name '_audit_block_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites.entry_id' '_entry.id' '_cell.entry_id' '_entry.id' '_cell_measurement.entry_id' '_entry.id' '_chemical.entry_id' '_entry.id' '_chemical_formula.entry_id' '_entry.id' '_computing.entry_id' '_entry.id' '_database.entry_id' '_entry.id' '_database_PDB_matrix.entry_id' '_entry.id' '_entry_link.entry_id' '_entry.id' '_exptl.entry_id' '_entry.id' '_geom.entry_id' '_entry.id' '_journal.entry_id' '_entry.id' '_phasing_averaging.entry_id' '_entry.id' '_phasing_isomorphous.entry_id' '_entry.id' '_phasing_MAD.entry_id' '_entry.id' '_phasing_MIR.entry_id' '_entry.id' '_publ.entry_id' '_entry.id' '_publ_manuscript_incl.entry_id' '_entry.id' '_refine.entry_id' '_entry.id' '_refine_analyze.entry_id' '_entry.id' '_reflns.entry_id' '_entry.id' '_struct.entry_id' '_entry.id' '_struct_keywords.entry_id' '_entry.id' '_struct_mon_details.entry_id' '_entry.id' '_symmetry.entry_id' '_entry.id' _item_type.code code save_ save_entry_link _category.description ; Data items in the ENTRY_LINK category record the relationships between the current data block identified by _entry.id and other data blocks within the current file which may be referenced in the current data block. ; _category.id entry_link _category.mandatory_code no loop_ _category_key.name '_entry_link.id' '_entry_link.entry_id' loop_ _category_group.id 'inclusive_group' 'entry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; ; loop_ _entry_link.id _entry_link.entry_id _entry_link.details KSE_COM KSE_TEXT 'experimental data common to ref./mod. structures' KSE_REF KSE_TEXT 'reference structure' KSE_MOD KSE_TEXT 'modulated structure' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entry_link.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_entry_link.entry_id' _item.mandatory_code yes save_ save__entry_link.id _item_description.description ; The value of _entry_link.id identifies a data block related to the current data block. ; _item.name '_entry_link.id' _item.category_id entry_link _item.mandatory_code yes _item_aliases.alias_name '_audit_link_block_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__entry_link.details _item_description.description ; A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id. ; _item.name '_entry_link.details' _item.category_id entry_link _item.mandatory_code no _item_aliases.alias_name '_audit_link_block_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ########### ## EXPTL ## ########### save_exptl _category.description ; Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. ; _category.id exptl _category.mandatory_code no _category_key.name '_exptl.entry_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. ; ; _exptl.entry_id datablock1 _exptl.absorpt_coefficient_mu 1.22 _exptl.absorpt_correction_T_max 0.896 _exptl.absorpt_correction_T_min 0.802 _exptl.absorpt_correction_type integration _exptl.absorpt_process_details ; Gaussian grid method from SHELX76 Sheldrick, G. M., "SHELX-76: structure determination and refinement program", Cambridge University, UK, 1976 ; _exptl.crystals_number 1 _exptl.details ; Enraf-Nonius LT2 liquid nitrogen variable-temperature device used ; _exptl.method 'single-crystal x-ray diffraction' _exptl.method_details ; graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl.absorpt_coefficient_mu _item_description.description ; The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. ; _item.name '_exptl.absorpt_coefficient_mu' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_coefficient_mu' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code reciprocal_millimetres save_ save__exptl.absorpt_correction_T_max _item_description.description ; The maximum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. ; _item.name '_exptl.absorpt_correction_T_max' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_T_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__exptl.absorpt_correction_T_min _item_description.description ; The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. ; _item.name '_exptl.absorpt_correction_T_min' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_T_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__exptl.absorpt_correction_type _item_description.description ; The absorption correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available. ; _item.name '_exptl.absorpt_correction_type' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail analytical 'analytical from crystal shape' cylinder 'cylindrical' empirical 'empirical from intensities' gaussian 'Gaussian from crystal shape' integration 'integration from crystal shape' multi-scan 'symmetry-related measurements' none 'no correction applied' numerical 'numerical from crystal shape' psi-scan 'psi-scan corrections' refdelf 'refined from delta-F' sphere 'spherical' save_ save__exptl.absorpt_process_details _item_description.description ; Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. ; _item.name '_exptl.absorpt_process_details' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_process_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Tompa analytical' save_ save__exptl.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_exptl.entry_id' _item.mandatory_code yes save_ save__exptl.crystals_number _item_description.description ; The total number of crystals used in the measurement of intensities. ; _item.name '_exptl.crystals_number' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_crystals_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__exptl.details _item_description.description ; Any special information about the experimental work prior to the intensity measurement. See also _exptl_crystal.preparation. ; _item.name '_exptl.details' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__exptl.method _item_description.description ; The method used in the experiment. ; _item.name '_exptl.method' _item.category_id exptl _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'single-crystal x-ray diffraction' 'single-crystal neutron diffraction' 'single-crystal electron diffraction' 'fiber x-ray diffraction' 'fiber neutron diffraction' 'fiber electron diffraction' 'single-crystal joint x-ray and neutron diffraction' 'single-crystal joint x-ray and electron diffraction' 'solution nmr' 'solid-state nmr' 'theoretical model' 'other' save_ save__exptl.method_details _item_description.description ; A description of special aspects of the experimental method. ; _item.name '_exptl.method_details' _item.category_id exptl _item.mandatory_code no _item_type.code text loop_ _item_examples.case '29 structures' 'minimized average structure' save_ ################### ## EXPTL_CRYSTAL ## ################### save_exptl_crystal _category.description ; Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density. ; _category.id exptl_crystal _category.mandatory_code no _category_key.name '_exptl_crystal.id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. ; ; _exptl_crystal.id xst2l _exptl_crystal.colour 'pale yellow' _exptl_crystal.density_diffrn 1.113 _exptl_crystal.density_Matthews 1.01 _exptl_crystal.density_meas 1.11 _exptl_crystal.density_meas_temp 294.5 _exptl_crystal.density_method 'neutral buoyancy' _exptl_crystal.density_percent_sol 0.15 # P = 1 - (1.23*N*MMass) / V _exptl_crystal.description 'hexagonal rod, uncut' _exptl_crystal.F_000 202 _exptl_crystal.preparation ; hanging drop, crystal soaked in 10% ethylene glycol for 10 h, then placed in nylon loop at data collection time ; _exptl_crystal.size_max 0.30 _exptl_crystal.size_mid 0.20 _exptl_crystal.size_min 0.05 _exptl_crystal.size_rad 0.025 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - using separate items to define upper and lower limits for a value. ; ; _exptl_crystal.density_meas_gt 2.5 _exptl_crystal.density_meas_lt 5.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 3 - here the density was measured at some unspecified temperature below room temperature. ; ; _exptl_crystal.density_meas_temp_lt 300 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal.colour _item_description.description ; The colour of the crystal. ; _item.name '_exptl_crystal.colour' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_colour' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'dark green' save_ save__exptl_crystal.density_diffrn _item_description.description ; Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). ; _item.name '_exptl_crystal.density_diffrn' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_diffrn' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__exptl_crystal.density_Matthews _item_description.description ; The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497. ; _item.name '_exptl_crystal.density_Matthews' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float save_ #save__exptl_crystal.density_meas # _item_description.description #; Density values measured using standard chemical and physical # methods. The units are megagrams per cubic metre (grams per # cubic centimetre). #; # _item.name '_exptl_crystal.density_meas' # _item.category_id exptl_crystal # _item.mandatory_code no # _item_aliases.alias_name '_exptl_crystal_density_meas' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_type.code float # save_ # #save__exptl_crystal.density_meas_temp # _item_description.description #; The temperature in kelvins at which _exptl_crystal.density_meas # was determined. #; # _item.name '_exptl_crystal.density_meas_temp' # _item.category_id exptl_crystal # _item.mandatory_code no # _item_aliases.alias_name '_exptl_crystal_density_meas_temp' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_type.code float # _item_units.code kelvins # save_ save__exptl_crystal.density_method _item_description.description ; The method used to measure _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_method' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__exptl_crystal.density_percent_sol _item_description.description ; Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule ; _item.name '_exptl_crystal.density_percent_sol' _item.category_id exptl_crystal _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__exptl_crystal.description _item_description.description ; A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces. ; _item.name '_exptl_crystal.description' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__exptl_crystal.F_000 _item_description.description ; The effective number of electrons in the crystal unit cell contributing to F(000). This may contain dispersion contributions and is calculated as F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 degree f~i~ = imaginary part of the scattering factors at theta = 0 degree the sum is taken over each atom in the unit cell ; _item.name '_exptl_crystal.F_000' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_F_000' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__exptl_crystal.id _item_description.description ; The value of _exptl_crystal.id must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_exptl_crystal.id' exptl_crystal yes '_exptl_crystal_face.crystal_id' exptl_crystal_face yes '_exptl_crystal_grow.crystal_id' exptl_crystal_grow yes '_exptl_crystal_grow_comp.crystal_id' exptl_crystal_grow_comp yes '_diffrn.crystal_id' diffrn yes '_refln.crystal_id' refln yes _item_aliases.alias_name '_exptl_crystal_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn.crystal_id' '_exptl_crystal.id' '_exptl_crystal_grow.crystal_id' '_exptl_crystal.id' '_exptl_crystal_face.crystal_id' '_exptl_crystal.id' '_exptl_crystal_grow_comp.crystal_id' '_exptl_crystal.id' '_refln.crystal_id' '_exptl_crystal.id' _item_type.code code save_ save__exptl_crystal.preparation _item_description.description ; Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. ; _item.name '_exptl_crystal.preparation' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_preparation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'mounted in an argon-filled quartz capillary' save_ save__exptl_crystal.size_max _item_description.description ; The maximum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_max' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__exptl_crystal.size_mid _item_description.description ; The medial dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_mid' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_mid' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__exptl_crystal.size_min _item_description.description ; The minimum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_min' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__exptl_crystal.size_rad _item_description.description ; The radius of the crystal, if the crystal is a sphere or a cylinder. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_rad' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_rad' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ ######################## ## EXPTL_CRYSTAL_FACE ## ######################## save_exptl_crystal_face _category.description ; Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. ; _category.id exptl_crystal_face _category.mandatory_code no loop_ _category_key.name '_exptl_crystal_face.crystal_id' '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_k' '_exptl_crystal_face.index_l' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4 for the 100 face of crystal xstl1. ; ; _exptl_crystal_face.crystal_id xstl1 _exptl_crystal_face.index_h 1 _exptl_crystal_face.index_k 0 _exptl_crystal_face.index_l 0 _exptl_crystal_face.diffr_chi 42.56 _exptl_crystal_face.diffr_kappa 30.23 _exptl_crystal_face.diffr_phi -125.56 _exptl_crystal_face.diffr_psi -0.34 _exptl_crystal_face.perp_dist 0.025 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal_face.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_exptl_crystal_face.crystal_id' _item.mandatory_code yes save_ save__exptl_crystal_face.diffr_chi _item_description.description ; The chi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_chi' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_chi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.diffr_kappa _item_description.description ; The kappa diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_kappa' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_kappa' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.diffr_phi _item_description.description ; The phi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_phi' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_phi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.diffr_psi _item_description.description ; The psi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_psi' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_psi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.index_h _item_description.description ; Miller index h of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_h' _item.category_id exptl_crystal_face _item.mandatory_code yes _item_aliases.alias_name '_exptl_crystal_face_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_k' '_exptl_crystal_face.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__exptl_crystal_face.index_k _item_description.description ; Miller index k of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_k' _item.category_id exptl_crystal_face _item.mandatory_code yes _item_aliases.alias_name '_exptl_crystal_face_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__exptl_crystal_face.index_l _item_description.description ; Miller index l of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_l' _item.category_id exptl_crystal_face _item.mandatory_code yes _item_aliases.alias_name '_exptl_crystal_face_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__exptl_crystal_face.perp_dist _item_description.description ; The perpendicular distance in millimetres from the face to the centre of rotation of the crystal. ; _item.name '_exptl_crystal_face.perp_dist' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_perp_dist' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ ######################## ## EXPTL_CRYSTAL_GROW ## ######################## save_exptl_crystal_grow _category.description ; Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal. ; _category.id exptl_crystal_grow _category.mandatory_code no _category_key.name '_exptl_crystal_grow.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'hanging drop' _exptl_crystal_grow.apparatus 'Linbro plates' _exptl_crystal_grow.atmosphere 'room air' _exptl_crystal_grow.pH 4.7 _exptl_crystal_grow.temp 18(3) _exptl_crystal_grow.time 'approximately 2 days' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal_grow.apparatus _item_description.description ; The physical apparatus in which the crystal was grown. ; _item.name '_exptl_crystal_grow.apparatus' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Linbro plate' 'sandwich box' 'ACA plates' save_ save__exptl_crystal_grow.atmosphere _item_description.description ; The nature of the gas or gas mixture in which the crystal was grown. ; _item.name '_exptl_crystal_grow.atmosphere' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'room air' 'nitrogen' 'argon' save_ save__exptl_crystal_grow.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_exptl_crystal_grow.crystal_id' _item.mandatory_code yes save_ save__exptl_crystal_grow.details _item_description.description ; A description of special aspects of the crystal growth. ; _item.name '_exptl_crystal_grow.details' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. ; ; Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. ; ; The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. ; save_ save__exptl_crystal_grow.method _item_description.description ; The method used to grow the crystals. ; _item.name '_exptl_crystal_grow.method' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'batch precipitation' 'batch dialysis' 'hanging drop vapor diffusion' 'sitting drop vapor diffusion' save_ save__exptl_crystal_grow.method_ref _item_description.description ; A literature reference that describes the method used to grow the crystals. ; _item.name '_exptl_crystal_grow.method_ref' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'McPherson et al., 1988' save_ save__exptl_crystal_grow.pH _item_description.description ; The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in _exptl_crystal_grow.details. ; _item.name '_exptl_crystal_grow.pH' _item.category_id exptl_crystal_grow _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float loop_ _item_examples.case 7.4 7.6 4.3 save_ save__exptl_crystal_grow.pressure _item_description.description ; The ambient pressure in kilopascals at which the crystal was grown. ; _item.name '_exptl_crystal_grow.pressure' _item.category_id exptl_crystal_grow _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_exptl_crystal_grow.pressure_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kilopascals save_ save__exptl_crystal_grow.pressure_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _exptl_crystal_grow.pressure. ; _item.name '_exptl_crystal_grow.pressure_esd' _item.category_id exptl_crystal_grow _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_exptl_crystal_grow.pressure' _item_related.function_code associated_value _item_type.code float _item_units.code kilopascals save_ save__exptl_crystal_grow.seeding _item_description.description ; A description of the protocol used for seeding the crystal growth. ; _item.name '_exptl_crystal_grow.seeding' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'macroseeding' ; Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. ; save_ save__exptl_crystal_grow.seeding_ref _item_description.description ; A literature reference that describes the protocol used to seed the crystal. ; _item.name '_exptl_crystal_grow.seeding_ref' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text _item_examples.case 'Stura et al., 1989' save_ save__exptl_crystal_grow.temp _item_description.description ; The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in _exptl_crystal_grow.details. ; _item.name '_exptl_crystal_grow.temp' _item.category_id exptl_crystal_grow _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_exptl_crystal_grow.temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvins save_ save__exptl_crystal_grow.temp_details _item_description.description ; A description of special aspects of temperature control during crystal growth. ; _item.name '_exptl_crystal_grow.temp_details' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text save_ save__exptl_crystal_grow.temp_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _exptl_crystal_grow.temp. ; _item.name '_exptl_crystal_grow.temp_esd' _item.category_id exptl_crystal_grow _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_exptl_crystal_grow.temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvins save_ save__exptl_crystal_grow.time _item_description.description ; The approximate time that the crystal took to grow to the size used for data collection. ; _item.name '_exptl_crystal_grow.time' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'overnight' '2-4 days' '6 months' save_ ############################# ## EXPTL_CRYSTAL_GROW_COMP ## ############################# save_exptl_crystal_grow_comp _category.description ; Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in _exptl_crystal_grow_comp.details using the solutions described in EXPTL_CRYSTAL_GROW_COMP. ; _category.id exptl_crystal_grow_comp _category.mandatory_code no loop_ _category_key.name '_exptl_crystal_grow_comp.id' '_exptl_crystal_grow_comp.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'HIV-1 protease' '0.002 ml' '6 mg/ml' ; The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide ; 1 2 2 'NaCl' '0.200 ml' '4 M' 'in 3 mM NaAzide' 1 3 2 'Acetic Acid' '0.047 ml' '100 mM' 'in 3 mM NaAzide' 1 4 2 'Na Acetate' '0.053 ml' '100 mM' ; in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. ; 1 5 2 'water' '0.700 ml' 'neat' 'in 3 mM NaAzide' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal_grow_comp.conc _item_description.description ; The concentration of the solution component. ; _item.name '_exptl_crystal_grow_comp.conc' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case '200 \ml' '0.1 ml' save_ save__exptl_crystal_grow_comp.details _item_description.description ; A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. ; _item.name '_exptl_crystal_grow_comp.details' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'in 3 mM NaAzide' ; The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide ; ; in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. ; save_ save__exptl_crystal_grow_comp.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_exptl_crystal_grow_comp.crystal_id' _item.mandatory_code yes save_ save__exptl_crystal_grow_comp.id _item_description.description ; The value of _exptl_crystal_grow_comp.id must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_exptl_crystal_grow_comp.id' _item.category_id exptl_crystal_grow_comp _item.mandatory_code yes _item_type.code line loop_ _item_examples.case '1' 'A' 'protein in buffer' save_ save__exptl_crystal_grow_comp.name _item_description.description ; A common name for the component of the solution. ; _item.name '_exptl_crystal_grow_comp.name' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'protein in buffer' 'acetic acid' save_ save__exptl_crystal_grow_comp.sol_id _item_description.description ; An identifier for the solution to which the given solution component belongs. ; _item.name '_exptl_crystal_grow_comp.sol_id' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case '1' 'well solution' 'solution A' save_ save__exptl_crystal_grow_comp.volume _item_description.description ; The volume of the solution component. ; _item.name '_exptl_crystal_grow_comp.volume' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case '200 \ml' '0.1 ml' save_ ########## ## GEOM ## ########## save_geom _category.description ; Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag. ; _category.id geom _category.mandatory_code no _category_key.name '_geom.entry_id' loop_ _category_group.id 'inclusive_group' 'geom_group' save_ save__geom.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_geom.entry_id' _item.mandatory_code yes save_ save__geom.details _item_description.description ; A description of geometry not covered by the existing data names in the GEOM categories, such as least-squares planes. ; _item.name '_geom.details' _item.category_id geom _item.mandatory_code no _item_aliases.alias_name '_geom_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ################ ## GEOM_ANGLE ## ################ save_geom_angle _category.description ; Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_angle _category.mandatory_code no loop_ _category_key.name '_geom_angle.atom_site_id_1' '_geom_angle.atom_site_id_2' '_geom_angle.atom_site_id_3' '_geom_angle.site_symmetry_1' '_geom_angle.site_symmetry_2' '_geom_angle.site_symmetry_3' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _geom_angle.atom_site_id_1 _geom_angle.atom_site_id_2 _geom_angle.atom_site_id_3 _geom_angle.value _geom_angle.value_esd _geom_angle.site_symmetry_1 _geom_angle.site_symmetry_2 _geom_angle.site_symmetry_3 _geom_angle.publ_flag C2 O1 C5 111.6 0.2 1_555 1_555 1_555 yes O1 C2 C3 110.9 0.2 1_555 1_555 1_555 yes O1 C2 O21 122.2 0.3 1_555 1_555 1_555 yes C3 C2 O21 127.0 0.3 1_555 1_555 1_555 yes C2 C3 N4 101.3 0.2 1_555 1_555 1_555 yes C2 C3 C31 111.3 0.2 1_555 1_555 1_555 yes C2 C3 H3 107 1 1_555 1_555 1_555 no N4 C3 C31 116.7 0.2 1_555 1_555 1_555 yes # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_angle.atom_site_id_1 _item_description.description ; The identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_angle.atom_site_id_2' '_geom_angle.atom_site_id_3' save_ save__geom_angle.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_id_2 _item_description.description ; The identifier of the second of the three atom sites that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_angle.atom_site_id_1' '_geom_angle.atom_site_id_3' save_ save__geom_angle.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_id_3 _item_description.description ; The identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_id_3' _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_atom_site_label_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_angle.atom_site_id_1' '_geom_angle.atom_site_id_2' save_ save__geom_angle.atom_site_label_alt_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_alt_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_atom_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_atom_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_comp_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_comp_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_seq_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_seq_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_asym_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_asym_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_atom_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_atom_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_asym_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_asym_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_comp_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_comp_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_seq_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_seq_id_3' _item.mandatory_code no save_ save__geom_angle.publ_flag _item_description.description ; This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles. ; _item.name '_geom_angle.publ_flag' _item.category_id geom_angle _item.mandatory_code no _item_aliases.alias_name '_geom_angle_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"' save_ save__geom_angle.site_symmetry_1 _item_description.description ; The symmetry code of the first of the three atom sites that define the angle. ; _item.name '_geom_angle.site_symmetry_1' _item.category_id geom_angle _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_angle.site_symmetry_2 _item_description.description ; The symmetry code of the second of the three atom sites that define the angle. ; _item.name '_geom_angle.site_symmetry_2' _item.category_id geom_angle _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_angle.site_symmetry_3 _item_description.description ; The symmetry code of the third of the three atom sites that define the angle. ; _item.name '_geom_angle.site_symmetry_3' _item.category_id geom_angle _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_site_symmetry_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_angle.value _item_description.description ; Angle in degrees defined by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and _geom_angle.atom_site_id_3. ; _item.name '_geom_angle.value' _item.category_id geom_angle _item.mandatory_code no _item_aliases.alias_name '_geom_angle' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_geom_angle.value_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__geom_angle.value_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_angle.value. ; _item.name '_geom_angle.value_esd' _item.category_id geom_angle _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_angle.value' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ ############### ## GEOM_BOND ## ############### save_geom_bond _category.description ; Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_bond _category.mandatory_code no loop_ _category_key.name '_geom_bond.atom_site_id_1' '_geom_bond.atom_site_id_2' '_geom_bond.site_symmetry_1' '_geom_bond.site_symmetry_2' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _geom_bond.atom_site_id_1 _geom_bond.atom_site_id_2 _geom_bond.dist _geom_bond.dist_esd _geom_bond.site_symmetry_1 _geom_bond.site_symmetry_2 _geom_bond.publ_flag O1 C2 1.342 0.004 1_555 1_555 yes O1 C5 1.439 0.003 1_555 1_555 yes C2 C3 1.512 0.004 1_555 1_555 yes C2 O21 1.199 0.004 1_555 1_555 yes C3 N4 1.465 0.003 1_555 1_555 yes C3 C31 1.537 0.004 1_555 1_555 yes C3 H3 1.00 0.03 1_555 1_555 no N4 C5 1.472 0.003 1_555 1_555 yes # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_bond.atom_site_id_1 _item_description.description ; The identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_bond.atom_site_id_2' save_ save__geom_bond.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_id_2 _item_description.description ; The identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_bond.atom_site_id_1' save_ save__geom_bond.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_bond.dist _item_description.description ; The intramolecular bond distance in angstroms. ; _item.name '_geom_bond.dist' _item.category_id geom_bond _item.mandatory_code no _item_aliases.alias_name '_geom_bond_distance' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_bond.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_bond.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_bond.dist. ; _item.name '_geom_bond.dist_esd' _item.category_id geom_bond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_bond.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_bond.publ_flag _item_description.description ; This code signals whether the bond distance is referred to in a publication or should be placed in a list of significant bond distances. ; _item.name '_geom_bond.publ_flag' _item.category_id geom_bond _item.mandatory_code no _item_aliases.alias_name '_geom_bond_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include bond in special list' n 'abbreviation for "no"' yes 'do include bond in special list' y 'abbreviation for "yes"' save_ save__geom_bond.site_symmetry_1 _item_description.description ; The symmetry code of the first of the two atom sites that define the bond. ; _item.name '_geom_bond.site_symmetry_1' _item.category_id geom_bond _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_bond.site_symmetry_2 _item_description.description ; The symmetry code of the second of the two atom sites that define the bond. ; _item.name '_geom_bond.site_symmetry_2' _item.category_id geom_bond _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ################## ## GEOM_CONTACT ## ################## save_geom_contact _category.description ; Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_contact _category.mandatory_code no loop_ _category_key.name '_geom_contact.atom_site_id_1' '_geom_contact.atom_site_id_2' '_geom_contact.site_symmetry_1' '_geom_contact.site_symmetry_2' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. ; ; loop_ _geom_contact.atom_site_id_1 _geom_contact.atom_site_id_2 _geom_contact.dist _geom_contact.dist_esd _geom_contact.site_symmetry_1 _geom_contact.site_symmetry_2 _geom_contact.publ_flag O(1) O(2) 2.735 0.003 . . yes H(O1) O(2) 1.82 . . . no ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_contact.atom_site_id_1 _item_description.description ; The identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_contact.atom_site_id_2' save_ save__geom_contact.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_id_2 _item_description.description ; The identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_contact.atom_site_id_1' save_ save__geom_contact.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_contact.dist _item_description.description ; The interatomic contact distance in angstroms. ; _item.name '_geom_contact.dist' _item.category_id geom_contact _item.mandatory_code no _item_aliases.alias_name '_geom_contact_distance' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_contact.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_contact.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_contact.dist. ; _item.name '_geom_contact.dist_esd' _item.category_id geom_contact _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_contact.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_contact.publ_flag _item_description.description ; This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances. ; _item.name '_geom_contact.publ_flag' _item.category_id geom_contact _item.mandatory_code no _item_aliases.alias_name '_geom_contact_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include distance in special list' n 'abbreviation for "no"' yes 'do include distance in special list' y 'abbreviation for "yes"' save_ save__geom_contact.site_symmetry_1 _item_description.description ; The symmetry code of the first of the two atom sites that define the contact. ; _item.name '_geom_contact.site_symmetry_1' _item.category_id geom_contact _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_contact.site_symmetry_2 _item_description.description ; The symmetry code of the second of the two atom sites that define the contact. ; _item.name '_geom_contact.site_symmetry_2' _item.category_id geom_contact _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ################ ## GEOM_HBOND ## ################ save_geom_hbond _category.description ; Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_hbond _category.mandatory_code no loop_ _category_key.name '_geom_hbond.atom_site_id_A' '_geom_hbond.atom_site_id_D' '_geom_hbond.atom_site_id_H' '_geom_hbond.site_symmetry_A' '_geom_hbond.site_symmetry_D' '_geom_hbond.site_symmetry_H' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. ; ; loop_ _geom_hbond.atom_site_id_D _geom_hbond.atom_site_id_H _geom_hbond.atom_site_id_A _geom_hbond.dist_DH _geom_hbond.dist_HA _geom_hbond.dist_DA _geom_hbond.angle_DHA _geom_hbond.publ_flag N6 HN6 OW 0.888 1.921 2.801 169.6 yes OW HO2 O7 0.917 1.923 2.793 153.5 yes OW HO1 N10 0.894 1.886 2.842 179.7 yes ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_hbond.angle_DHA _item_description.description ; The angle in degrees defined by the donor-, hydrogen- and acceptor-atom sites in a hydrogen bond. ; _item.name '_geom_hbond.angle_DHA' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_angle_DHA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.angle_DHA_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.angle_DHA_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_hbond.angle_DHA. ; _item.name '_geom_hbond.angle_DHA_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.angle_DHA' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.atom_site_id_A _item_description.description ; The identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_id_A' _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_atom_site_label_A' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_hbond.atom_site_id_D' '_geom_hbond.atom_site_id_H' save_ save__geom_hbond.atom_site_label_alt_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_alt_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_asym_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_asym_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_atom_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_atom_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_comp_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_comp_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_seq_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_seq_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_id_D _item_description.description ; The identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_id_D' _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_atom_site_label_D' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_hbond.atom_site_id_A' '_geom_hbond.atom_site_id_H' save_ save__geom_hbond.atom_site_label_alt_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_alt_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_asym_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_asym_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_atom_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_atom_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_comp_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_comp_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_seq_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_seq_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_id_H _item_description.description ; The identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_id_H' _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_atom_site_label_H' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_hbond.atom_site_id_A' '_geom_hbond.atom_site_id_D' save_ save__geom_hbond.atom_site_label_alt_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_alt_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_asym_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_asym_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_atom_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_atom_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_comp_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_comp_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_seq_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_seq_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_asym_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_asym_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_atom_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_atom_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_comp_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_comp_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_seq_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_seq_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_asym_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_asym_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_atom_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_atom_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_comp_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_comp_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_seq_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_seq_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_asym_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_asym_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_atom_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_atom_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_comp_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_comp_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_seq_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_seq_id_H' _item.mandatory_code no save_ save__geom_hbond.dist_DA _item_description.description ; The distance in angstroms between the donor- and acceptor-atom sites in a hydrogen bond. ; _item.name '_geom_hbond.dist_DA' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_distance_DA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.dist_DA_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.dist_DA_esd _item_description.description ; The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_DA. ; _item.name '_geom_hbond.dist_DA_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.dist_DH' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.dist_DH _item_description.description ; The distance in angstroms between the donor- and hydrogen-atom sites in a hydrogen bond. ; _item.name '_geom_hbond.dist_DH' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_distance_DH' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.dist_DH_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.dist_DH_esd _item_description.description ; The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_DH. ; _item.name '_geom_hbond.dist_DH_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.dist_DH' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.dist_HA _item_description.description ; The distance in angstroms between the hydrogen- and acceptor- atom sites in a hydrogen bond. ; _item.name '_geom_hbond.dist_HA' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_distance_HA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.dist_HA_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.dist_HA_esd _item_description.description ; The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_HA. ; _item.name '_geom_hbond.dist_HA_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.dist_HA' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.publ_flag _item_description.description ; This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry. ; _item.name '_geom_hbond.publ_flag' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include bond in special list' n 'abbreviation for "no"' yes 'do include bond in special list' y 'abbreviation for "yes"' save_ save__geom_hbond.site_symmetry_A _item_description.description ; The symmetry code of the acceptor-atom site that defines the hydrogen bond. ; _item.name '_geom_hbond.site_symmetry_A' _item.category_id geom_hbond _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_site_symmetry_A' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_hbond.site_symmetry_D _item_description.description ; The symmetry code of the donor-atom site that defines the hydrogen bond. ; _item.name '_geom_hbond.site_symmetry_D' _item.category_id geom_hbond _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_site_symmetry_D' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_hbond.site_symmetry_H _item_description.description ; The symmetry code of the hydrogen-atom site that defines the hydrogen bond. ; _item.name '_geom_hbond.site_symmetry_H' _item.category_id geom_hbond _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_site_symmetry_H' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ################## ## GEOM_TORSION ## ################## save_geom_torsion _category.description ; Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction _geom_torsion.atom_site_id_2 to _geom_torsion.atom_site_id_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. ; _category.id geom_torsion _category.mandatory_code no loop_ _category_key.name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_3' '_geom_torsion.atom_site_id_4' '_geom_torsion.site_symmetry_1' '_geom_torsion.site_symmetry_2' '_geom_torsion.site_symmetry_3' '_geom_torsion.site_symmetry_4' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. ; ; loop_ _geom_torsion.atom_site_id_1 _geom_torsion.atom_site_id_2 _geom_torsion.atom_site_id_3 _geom_torsion.atom_site_id_4 _geom_torsion.value _geom_torsion.site_symmetry_1 _geom_torsion.site_symmetry_2 _geom_torsion.site_symmetry_3 _geom_torsion.site_symmetry_4 _geom_torsion.publ_flag C(9) O(2) C(7) C(2) 71.8 . . . . yes C(7) O(2) C(9) C(10) -168.0 . . . 2_666 yes C(10) O(3) C(8) C(6) -167.7 . . . . yes C(8) O(3) C(10) C(9) -69.7 . . . 2_666 yes O(1) C(1) C(2) C(3) -179.5 . . . . no O(1) C(1) C(2) C(7) -0.6 . . . . no ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_torsion.atom_site_id_1 _item_description.description ; The identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_3' '_geom_torsion.atom_site_id_4' save_ save__geom_torsion.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_id_2 _item_description.description ; The identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_3' '_geom_torsion.atom_site_id_4' save_ save__geom_torsion.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_id_3 _item_description.description ; The identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_3' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_4' save_ save__geom_torsion.atom_site_label_alt_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_id_4 _item_description.description ; The identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_4' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_3' save_ save__geom_torsion.atom_site_label_alt_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_4' _item.mandatory_code no save_ save__geom_torsion.publ_flag _item_description.description ; This code signals whether the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles. ; _item.name '_geom_torsion.publ_flag' _item.category_id geom_torsion _item.mandatory_code no _item_aliases.alias_name '_geom_torsion_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"' save_ save__geom_torsion.site_symmetry_1 _item_description.description ; The symmetry code of the first of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_1' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.site_symmetry_2 _item_description.description ; The symmetry code of the second of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_2' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.site_symmetry_3 _item_description.description ; The symmetry code of the third of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_3' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.site_symmetry_4 _item_description.description ; The symmetry code of the fourth of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_4' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.value _item_description.description ; The value of the torsion angle in degrees. ; _item.name '_geom_torsion.value' _item.category_id geom_torsion _item.mandatory_code no _item_aliases.alias_name '_geom_torsion' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_geom_torsion.value_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__geom_torsion.value_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_torsion.value. ; _item.name '_geom_torsion.value_esd' _item.category_id geom_torsion _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_torsion.value' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ ############# ## JOURNAL ## ############# save_journal _category.description ; Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only. ; _category.id journal _category.mandatory_code no _category_key.name '_journal.entry_id' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. ; ; _journal.entry_id 'TOZ' _journal.date_recd_electronic 1991-04-15 _journal.date_from_coeditor 1991-04-18 _journal.date_accepted 1991-04-18 _journal.date_printers_first 1991-08-07 _journal.date_proofs_out 1991-08-07 _journal.coeditor_code HL0007 _journal.techeditor_code C910963 _journal.coden_ASTM ACSCEE _journal.name_full 'Acta Crystallographica Section C' _journal.year 1991 _journal.volume 47 _journal.issue NOV91 _journal.page_first 2276 _journal.page_last 2277 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__journal.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_journal.entry_id' _item.mandatory_code yes save_ save__journal.coden_ASTM _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_ASTM' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coden_ASTM' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coden_Cambridge _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_Cambridge' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coden_Cambridge' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_address _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_address' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.coeditor_code _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_code' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_email _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_email' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_fax _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_fax' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_name _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_name' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_notes _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_notes' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_notes' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.coeditor_phone _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_phone' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.data_validation_number _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.data_validation_number' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_data_validation_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__journal.date_accepted _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_accepted' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_accepted' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_from_coeditor _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_from_coeditor' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_from_coeditor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_to_coeditor _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_to_coeditor' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_to_coeditor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_printers_final _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_final' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_final' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_printers_first _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_first' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_first' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_proofs_in _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_in' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_in' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_proofs_out _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_out' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_out' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_recd_copyright _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_copyright' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_copyright' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_recd_electronic _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_electronic' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_electronic' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_recd_hard_copy _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_hard_copy' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_hard_copy' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.issue _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.issue' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_issue' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.language _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.language' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_language' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.name_full _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.name_full' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_name_full' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.page_first _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_first' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_page_first' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.page_last _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_last' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_page_last' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.paper_category _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.paper_category' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_paper_category' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.suppl_publ_number _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_number' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.suppl_publ_pages _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_pages' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_pages' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_address _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_address' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.techeditor_code _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_code' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_email _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_email' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_fax _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_fax' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_name _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_name' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_notes _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_notes' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_notes' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.techeditor_phone _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_phone' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.volume _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.volume' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_volume' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.year _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.year' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_year' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ################### ## JOURNAL_INDEX ## ################### save_journal_index _category.description ; Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items. ; _category.id journal_index _category.mandatory_code no loop_ _category_key.name '_journal_index.type' '_journal_index.term' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [Acta Cryst. (1994), C50, 2067-2069]. ; ; loop_ _journal_index.type _journal_index.term _journal_index.subterm O C16H19NO4 . S alkaloids (-)-norcocaine S (-)-norcocaine . S ; [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate ; . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__journal_index.subterm _item_description.description ; Journal index data items are defined by the journal staff. ; _item.name '_journal_index.subterm' _item.category_id journal_index _item.mandatory_code no _item_aliases.alias_name '_journal_index_subterm' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal_index.term _item_description.description ; Journal index data items are defined by the journal staff. ; _item.name '_journal_index.term' _item.category_id journal_index _item.mandatory_code no _item_aliases.alias_name '_journal_index_term' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal_index.type _item_description.description ; Journal index data items are defined by the journal staff. ; _item.name '_journal_index.type' _item.category_id journal_index _item.mandatory_code no _item_aliases.alias_name '_journal_index_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ############# ## PHASING ## ############# save_phasing _category.description ; Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories. ; _category.id phasing _category.mandatory_code no _category_key.name '_phasing.method' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _phasing.method 'mir' 'averaging' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing.method _item_description.description ; A listing of the method or methods used to phase this structure. ; _item.name '_phasing.method' _item.category_id phasing _item.mandatory_code yes _item_type.code ucode loop_ _item_examples.case _item_examples.detail abinitio ; phasing by ab initio methods ; averaging ; phase improvement by averaging over multiple images of the structure ; dm ; phasing by direct methods ; isas ; phasing by iterative single-wavelength anomalous scattering ; isir ; phasing by iterative single-wavelength isomorphous replacement ; isomorphous ; phasing beginning with phases calculated from an isomorphous structure ; mad ; phasing by multiple-wavelength anomalous dispersion ; mir ; phasing by multiple isomorphous replacement ; miras ; phasing by multiple isomorphous replacement with anomalous scattering ; mr ; phasing by molecular replacement ; sir ; phasing by single isomorphous replacement ; siras ; phasing by single isomorphous replacement with anomalous scattering ; save_ ####################### ## PHASING_AVERAGING ## ####################### save_phasing_averaging _category.description ; Data items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved. ; _category.id phasing_averaging _category.mandatory_code no _category_key.name '_phasing_averaging.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; _phasing_averaging.entry_id 'EXAMHYPO' _phasing_averaging.method ; Iterative threefold averaging alternating with phase extensions by 0.5 reciprocal lattice units per cycle. ; _phasing_averaging.details ; The position of the threefold axis was redetermined every five cycles. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_averaging.details _item_description.description ; A description of special aspects of the averaging process. ; _item.name '_phasing_averaging.details' _item.category_id phasing_averaging _item.mandatory_code no _item_type.code text save_ save__phasing_averaging.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_averaging.entry_id' _item.mandatory_code yes save_ save__phasing_averaging.method _item_description.description ; A description of the phase-averaging phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the phase-averaging program. ; _item.name '_phasing_averaging.method' _item.category_id phasing_averaging _item.mandatory_code no _item_type.code text save_ ######################### ## PHASING_ISOMORPHOUS ## ######################### save_phasing_isomorphous _category.description ; Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases. ; _category.id phasing_isomorphous _category.mandatory_code no _category_key.name '_phasing_isomorphous.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 4PHV and laboratory records for the structure corresponding to PDB entry 4PHV. ; ; _phasing_isomorphous.parent 'PDB entry 5HVP' _phasing_isomorphous.details ; The inhibitor and all solvent atoms were removed from the parent structure before beginning refinement. All static disorder present in the parent structure was also removed. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_isomorphous.details _item_description.description ; A description of special aspects of the isomorphous phasing. ; _item.name '_phasing_isomorphous.details' _item.category_id phasing_isomorphous _item.mandatory_code no _item_type.code text _item_examples.case ; Residues 13-18 were eliminated from the starting model as it was anticipated that binding of the inhibitor would cause a structural rearrangement in this part of the structure. ; save_ save__phasing_isomorphous.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_isomorphous.entry_id' _item.mandatory_code yes save_ save__phasing_isomorphous.method _item_description.description ; A description of the isomorphous-phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the isomorphous phasing program. ; _item.name '_phasing_isomorphous.method' _item.category_id phasing_isomorphous _item.mandatory_code no _item_type.code text _item_examples.case ; Iterative threefold averaging alternating with phase extension by 0.5 reciprocal lattice units per cycle. ; save_ save__phasing_isomorphous.parent _item_description.description ; Reference to the structure used to generate starting phases if the structure referenced in this data block was phased by virtue of being isomorphous to a known structure (e.g. a mutant that crystallizes in the same space group as the wild-type protein.) ; _item.name '_phasing_isomorphous.parent' _item.category_id phasing_isomorphous _item.mandatory_code no _item_type.code text save_ ################# ## PHASING_MAD ## ################# save_phasing_MAD _category.description ; Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved. ; _category.id phasing_MAD _category.mandatory_code no _category_key.name '_phasing_MAD.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; _phasing_MAD.entry_id 'NCAD' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD.details _item_description.description ; A description of special aspects of the MAD phasing. ; _item.name '_phasing_MAD.details' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code text save_ save__phasing_MAD.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_MAD.entry_id' _item.mandatory_code yes save_ save__phasing_MAD.method _item_description.description ; A description of the MAD phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MAD phasing program. ; _item.name '_phasing_MAD.method' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code text save_ ####################### ## PHASING_MAD_CLUST ## ####################### save_phasing_MAD_clust _category.description ; Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases. ; _category.id phasing_MAD_clust _category.mandatory_code no loop_ _category_key.name '_phasing_MAD_clust.expt_id' '_phasing_MAD_clust.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_clust.id _phasing_MAD_clust.expt_id _phasing_MAD_clust.number_set '4 wavelength' 1 4 '5 wavelength' 1 5 '5 wavelength' 2 5 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_clust.expt_id _item_description.description ; This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category. ; _item.name '_phasing_MAD_clust.expt_id' _item.mandatory_code yes save_ save__phasing_MAD_clust.id _item_description.description ; The value of _phasing_MAD_clust.id must, together with _phasing_MAD_clust.expt_id, uniquely identify a record in the PHASING_MAD_CLUST list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MAD_clust.id' phasing_MAD_clust yes '_phasing_MAD_set.clust_id' phasing_MAD_set yes '_phasing_MAD_ratio.clust_id' phasing_MAD_ratio yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MAD_set.clust_id' '_phasing_MAD_clust.id' '_phasing_MAD_ratio.clust_id' '_phasing_MAD_clust.id' _item_type.code code save_ save__phasing_MAD_clust.number_set _item_description.description ; The number of data sets in this cluster of data sets. ; _item.name '_phasing_MAD_clust.number_set' _item.category_id phasing_MAD_clust _item.mandatory_code no _item_type.code int save_ ###################### ## PHASING_MAD_EXPT ## ###################### save_phasing_MAD_expt _category.description ; Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases. ; _category.id phasing_MAD_expt _category.mandatory_code no _category_key.name '_phasing_MAD_expt.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_expt.id _phasing_MAD_expt.number_clust _phasing_MAD_expt.R_normal_all _phasing_MAD_expt.R_normal_anom_scat _phasing_MAD_expt.delta_delta_phi _phasing_MAD_expt.delta_phi_sigma _phasing_MAD_expt.mean_fom 1 2 0.063 0.451 58.5 20.3 0.88 2 1 0.051 0.419 36.8 18.2 0.93 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_expt.delta_delta_phi _item_description.description ; The difference between two independent determinations of _phasing_MAD_expt.delta_phi. ; _item.name '_phasing_MAD_expt.delta_delta_phi' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_expt.delta_phi _item_description.description ; The phase difference between F~t~(h), the structure factor due to normal scattering from all atoms, and F~a~(h), the structure factor due to normal scattering from only the anomalous scatterers. ; _item.name '_phasing_MAD_expt.delta_phi' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float _item_related.related_name '_phasing_MAD_expt.delta_phi_sigma' _item_related.function_code associated_esd save_ save__phasing_MAD_expt.delta_phi_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MAD_expt.delta_phi. ; _item.name '_phasing_MAD_expt.delta_phi_sigma' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_related.related_name '_phasing_MAD_expt.delta_phi' _item_related.function_code associated_value _item_type.code float save_ save__phasing_MAD_expt.id _item_description.description ; The value of _phasing_MAD_expt.id must uniquely identify each record in the PHASING_MAD_EXPT list. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MAD_expt.id' phasing_MAD_expt yes '_phasing_MAD_clust.expt_id' phasing_MAD_clust yes '_phasing_MAD_set.expt_id' phasing_MAD_set yes '_phasing_MAD_ratio.expt_id' phasing_MAD_ratio yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MAD_clust.expt_id' '_phasing_MAD_expt.id' '_phasing_MAD_set.expt_id' '_phasing_MAD_expt.id' '_phasing_MAD_ratio.expt_id' '_phasing_MAD_expt.id' _item_type.code code save_ save__phasing_MAD_expt.mean_fom _item_description.description ; The mean figure of merit. ; _item.name '_phasing_MAD_expt.mean_fom' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_expt.number_clust _item_description.description ; The number of clusters of data sets in this phasing experiment. ; _item.name '_phasing_MAD_expt.number_clust' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code int save_ save__phasing_MAD_expt.R_normal_all _item_description.description ; Definition... ; _item.name '_phasing_MAD_expt.R_normal_all' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_expt.R_normal_anom_scat _item_description.description ; Definition... ; _item.name '_phasing_MAD_expt.R_normal_anom_scat' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ ####################### ## PHASING_MAD_RATIO ## ####################### save_phasing_MAD_ratio _category.description ; Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution. ; _category.id phasing_MAD_ratio _category.mandatory_code no loop_ _category_key.name '_phasing_MAD_ratio.clust_id' '_phasing_MAD_ratio.expt_id' '_phasing_MAD_ratio.wavelength_1' '_phasing_MAD_ratio.wavelength_2' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_ratio.expt_id _phasing_MAD_ratio.clust_id _phasing_MAD_ratio.wavelength_1 _phasing_MAD_ratio.wavelength_2 _phasing_MAD_ratio.d_res_low _phasing_MAD_ratio.d_res_high _phasing_MAD_ratio.ratio_two_wl _phasing_MAD_ratio.ratio_one_wl _phasing_MAD_ratio.ratio_one_wl_centric 1 '4 wavelength' 1.4013 1.4013 20.00 4.00 . 0.084 0.076 1 '4 wavelength' 1.4013 1.3857 20.00 4.00 0.067 . . 1 '4 wavelength' 1.4013 1.3852 20.00 4.00 0.051 . . 1 '4 wavelength' 1.4013 1.3847 20.00 4.00 0.044 . . 1 '4 wavelength' 1.3857 1.3857 20.00 4.00 . 0.110 0.049 1 '4 wavelength' 1.3857 1.3852 20.00 4.00 0.049 . . 1 '4 wavelength' 1.3857 1.3847 20.00 4.00 0.067 . . 1 '4 wavelength' 1.3852 1.3852 20.00 4.00 . 0.149 0.072 1 '4 wavelength' 1.3852 1.3847 20.00 4.00 0.039 . . 1 '4 wavelength' 1.3847 1.3847 20.00 4.00 . 0.102 0.071 1 '4 wavelength' 1.4013 1.4013 4.00 3.00 . 0.114 0.111 1 '4 wavelength' 1.4013 1.3857 4.00 3.00 0.089 . . 1 '4 wavelength' 1.4013 1.3852 4.00 3.00 0.086 . . 1 '4 wavelength' 1.4013 1.3847 4.00 3.00 0.077 . . 1 '4 wavelength' 1.3857 1.3857 4.00 3.00 . 0.140 0.127 1 '4 wavelength' 1.3857 1.3852 4.00 3.00 0.085 . . 1 '4 wavelength' 1.3857 1.3847 4.00 3.00 0.089 . . 1 '4 wavelength' 1.3852 1.3852 4.00 3.00 . 0.155 0.119 1 '4 wavelength' 1.3852 1.3847 4.00 3.00 0.082 . . 1 '4 wavelength' 1.3847 1.3847 4.00 3.00 . 0.124 0.120 1 '5 wavelength' 1.3857 1.3857 20.00 4.00 . 0.075 0.027 1 '5 wavelength' 1.3857 1.3852 20.00 4.00 0.041 . . 1 '5 wavelength' 1.3857 1.3847 20.00 4.00 0.060 . . 1 '5 wavelength' 1.3857 1.3784 20.00 4.00 0.057 . . 1 '5 wavelength' 1.3857 1.2862 20.00 4.00 0.072 . . 1 '5 wavelength' 1.3852 1.3852 20.00 4.00 . 0.105 0.032 1 '5 wavelength' 1.3852 1.3847 20.00 4.00 0.036 . . 1 '5 wavelength' 1.3852 1.3784 20.00 4.00 0.044 . . 1 '5 wavelength' 1.3852 1.2862 20.00 4.00 0.065 . . 1 '5 wavelength' 1.3847 1.3847 20.00 4.00 . 0.072 0.031 1 '5 wavelength' 1.3847 1.3784 20.00 4.00 0.040 . . 1 '5 wavelength' 1.3847 1.2862 20.00 4.00 0.059 . . 1 '5 wavelength' 1.3784 1.3784 20.00 4.00 . 0.059 0.032 1 '5 wavelength' 1.3784 1.2862 20.00 4.00 0.059 . . 1 '5 wavelength' 1.2862 1.3847 20.00 4.00 . 0.058 0.028 1 '5 wavelength' 1.3857 1.3857 4.00 3.00 . 0.078 0.075 1 '5 wavelength' 1.3857 1.3852 4.00 3.00 0.059 . . 1 '5 wavelength' 1.3857 1.3847 4.00 3.00 0.067 . . 1 '5 wavelength' 1.3857 1.3784 4.00 3.00 0.084 . . 1 '5 wavelength' 1.3857 1.2862 4.00 3.00 0.073 . . 1 '5 wavelength' 1.3852 1.3852 4.00 3.00 . 0.101 0.088 1 '5 wavelength' 1.3852 1.3847 4.00 3.00 0.066 . . 1 '5 wavelength' 1.3852 1.3784 4.00 3.00 0.082 . . 1 '5 wavelength' 1.3852 1.2862 4.00 3.00 0.085 . . 1 '5 wavelength' 1.3847 1.3847 4.00 3.00 . 0.097 0.074 1 '5 wavelength' 1.3847 1.3784 4.00 3.00 0.081 . . 1 '5 wavelength' 1.3847 1.2862 4.00 3.00 0.085 . . 1 '5 wavelength' 1.3784 1.3784 4.00 3.00 . 0.114 0.089 1 '5 wavelength' 1.3784 1.2862 4.00 3.00 0.103 . . 1 '5 wavelength' 1.2862 1.2862 4.00 3.00 . 0.062 0.060 2 '5 wavelength' 0.7263 0.7263 15.00 3.00 . 0.035 0.026 2 '5 wavelength' 0.7263 0.7251 15.00 3.00 0.028 . . 2 '5 wavelength' 0.7263 0.7284 15.00 3.00 0.023 . . 2 '5 wavelength' 0.7263 0.7246 15.00 3.00 0.025 . . 2 '5 wavelength' 0.7263 0.7217 15.00 3.00 0.026 . . 2 '5 wavelength' 0.7251 0.7251 15.00 3.00 . 0.060 0.026 2 '5 wavelength' 0.7251 0.7284 15.00 3.00 0.029 . . 2 '5 wavelength' 0.7251 0.7246 15.00 3.00 0.031 . . 2 '5 wavelength' 0.7251 0.7217 15.00 3.00 0.035 . . 2 '5 wavelength' 0.7284 0.7284 15.00 3.00 . 0.075 0.030 2 '5 wavelength' 0.7284 0.7246 15.00 3.00 0.023 . . 2 '5 wavelength' 0.7284 0.7217 15.00 3.00 0.027 . . 2 '5 wavelength' 0.7246 0.7246 15.00 3.00 . 0.069 0.026 2 '5 wavelength' 0.7246 0.7217 15.00 3.00 0.024 . . 2 '5 wavelength' 0.7217 0.7284 15.00 3.00 . 0.060 0.028 2 '5 wavelength' 0.7263 0.7263 3.00 1.90 . 0.060 0.050 2 '5 wavelength' 0.7263 0.7251 3.00 1.90 0.056 . . 2 '5 wavelength' 0.7263 0.7284 3.00 1.90 0.055 . . 2 '5 wavelength' 0.7263 0.7246 3.00 1.90 0.053 . . 2 '5 wavelength' 0.7263 0.7217 3.00 1.90 0.056 . . 2 '5 wavelength' 0.7251 0.7251 3.00 1.90 . 0.089 0.050 2 '5 wavelength' 0.7251 0.7284 3.00 1.90 0.054 . . 2 '5 wavelength' 0.7251 0.7246 3.00 1.90 0.058 . . 2 '5 wavelength' 0.7251 0.7217 3.00 1.90 0.063 . . 2 '5 wavelength' 0.7284 0.7284 3.00 1.90 . 0.104 0.057 2 '5 wavelength' 0.7284 0.7246 3.00 1.90 0.052 . . 2 '5 wavelength' 0.7284 0.7217 3.00 1.90 0.057 . . 2 '5 wavelength' 0.7246 0.7246 3.00 1.90 . 0.098 0.052 2 '5 wavelength' 0.7246 0.7217 3.00 1.90 0.054 . . 2 '5 wavelength' 0.7217 0.7284 3.00 1.90 . 0.089 0.060 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_ratio.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the highest resolution. ; _item.name '_phasing_MAD_ratio.d_res_high' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the lowest resolution. ; _item.name '_phasing_MAD_ratio.d_res_low' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.expt_id _item_description.description ; This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category. ; _item.name '_phasing_MAD_ratio.expt_id' _item.mandatory_code yes save_ save__phasing_MAD_ratio.clust_id _item_description.description ; This data item is a pointer to _phasing_MAD_clust.id in the PHASING_MAD_CLUST category. ; _item.name '_phasing_MAD_ratio.clust_id' _item.mandatory_code yes save_ save__phasing_MAD_ratio.ratio_one_wl _item_description.description ; The root-mean-square Bijvoet difference at one wavelength for all reflections. ; _item.name '_phasing_MAD_ratio.ratio_one_wl' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.ratio_one_wl_centric _item_description.description ; The root-mean-square Bijvoet difference at one wavelength for centric reflections. This would be equal to zero for perfect data and thus serves as an estimate of the noise in the anomalous signals. ; _item.name '_phasing_MAD_ratio.ratio_one_wl_centric' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.ratio_two_wl _item_description.description ; The root-mean-square dispersive Bijvoet difference between two wavelengths for all reflections. ; _item.name '_phasing_MAD_ratio.ratio_two_wl' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.wavelength_1 _item_description.description ; This data item is a pointer to _phasing_MAD_set.wavelength in the PHASING_MAD_SET category. ; _item.name '_phasing_MAD_ratio.wavelength_1' _item.mandatory_code yes save_ save__phasing_MAD_ratio.wavelength_2 _item_description.description ; This data item is a pointer to _phasing_MAD_set.wavelength in the PHASING_MAD_SET category. ; _item.name '_phasing_MAD_ratio.wavelength_2' _item.mandatory_code yes save_ ##################### ## PHASING_MAD_SET ## ##################### save_phasing_MAD_set _category.description ; Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment. ; _category.id phasing_MAD_set _category.mandatory_code no loop_ _category_key.name '_phasing_MAD_set.expt_id' '_phasing_MAD_set.clust_id' '_phasing_MAD_set.set_id' '_phasing_MAD_set.wavelength' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_set.expt_id _phasing_MAD_set.clust_id _phasing_MAD_set.set_id _phasing_MAD_set.wavelength _phasing_MAD_set.wavelength_details _phasing_MAD_set.d_res_low _phasing_MAD_set.d_res_high _phasing_MAD_set.f_prime _phasing_MAD_set.f_double_prime 1 '4 wavelength' aa 1.4013 'pre-edge' 20.00 3.00 -12.48 3.80 1 '4 wavelength' bb 1.3857 'peak' 20.00 3.00 -31.22 17.20 1 '4 wavelength' cc 1.3852 'edge' 20.00 3.00 -13.97 29.17 1 '4 wavelength' dd 1.3847 'remote' 20.00 3.00 -6.67 17.34 1 '5 wavelength' ee 1.3857 'ascending edge' 20.00 3.00 -28.33 14.84 1 '5 wavelength' ff 1.3852 'peak' 20.00 3.00 -21.50 30.23 1 '5 wavelength' gg 1.3847 'descending edge' 20.00 3.00 -10.71 20.35 1 '5 wavelength' hh 1.3784 'remote 1' 20.00 3.00 -14.45 11.84 1 '5 wavelength' ii 1.2862 'remote 2' 20.00 3.00 -9.03 9.01 2 '5 wavelength' jj 0.7263 'pre-edge' 15.00 1.90 -21.10 4.08 2 '5 wavelength' kk 0.7251 'edge' 15.00 1.90 -34.72 7.92 2 '5 wavelength' ll 0.7248 'peak' 15.00 1.90 -24.87 10.30 2 '5 wavelength' mm 0.7246 'descending edge' 15.00 1.90 -17.43 9.62 2 '5 wavelength' nn 0.7217 'remote' 15.00 1.90 -13.26 8.40 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_set.clust_id _item_description.description ; This data item is a pointer to _phasing_MAD_clust.id in the PHASING_MAD_CLUST category. ; _item.name '_phasing_MAD_set.clust_id' _item.mandatory_code yes save_ save__phasing_MAD_set.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data used for this set of data. This is called the highest resolution. ; _item.name '_phasing_MAD_set.d_res_high' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data used for this set of data. This is called the lowest resolution. ; _item.name '_phasing_MAD_set.d_res_low' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.expt_id _item_description.description ; This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category. ; _item.name '_phasing_MAD_set.expt_id' _item.mandatory_code yes save_ save__phasing_MAD_set.f_double_prime _item_description.description ; The f'' component of the anomalous scattering factor for this wavelength. ; _item.name '_phasing_MAD_set.f_double_prime' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.f_prime _item_description.description ; The f' component of the anomalous scattering factor for this wavelength. ; _item.name '_phasing_MAD_set.f_prime' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.set_id _item_description.description ; This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MAD_set.set_id' _item.mandatory_code yes save_ save__phasing_MAD_set.wavelength _item_description.description ; The wavelength at which this data set was measured. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MAD_set.wavelength' phasing_MAD_set yes '_phasing_MAD_ratio.wavelength_1' phasing_MAD_ratio yes '_phasing_MAD_ratio.wavelength_2' phasing_MAD_ratio yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MAD_ratio.wavelength_1' '_phasing_MAD_set.wavelength' '_phasing_MAD_ratio.wavelength_2' '_phasing_MAD_set.wavelength' _item_type.code float save_ save__phasing_MAD_set.wavelength_details _item_description.description ; A descriptor for this wavelength in this cluster of data sets. ; _item.name '_phasing_MAD_set.wavelength_details' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'peak' 'remote' 'ascending edge' save_ ################# ## PHASING_MIR ## ################# save_phasing_MIR _category.description ; Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS). ; _category.id phasing_MIR _category.mandatory_code no _category_key.name '_phasing_MIR.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. ; ; _phasing_MIR.method ; Standard phase refinement (Blow & Crick, 1959) ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR.details _item_description.description ; A description of special aspects of the isomorphous-replacement phasing. ; _item.name '_phasing_MIR.details' _item.category_id phasing_MIR _item.mandatory_code no _item_type.code text save_ save__phasing_MIR.d_res_high _item_description.description ; The lowest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the highest resolution. ; _item.name '_phasing_MIR.d_res_high' _item.category_id phasing_MIR _item.mandatory_code yes _item_aliases.alias_name '_phasing_MIR.ebi_d_res_high' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR.d_res_low _item_description.description ; The highest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the lowest resolution. ; _item.name '_phasing_MIR.d_res_low' _item.category_id phasing_MIR _item.mandatory_code yes _item_aliases.alias_name '_phasing_MIR.ebi_d_res_low' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_MIR.entry_id' _item.mandatory_code yes save_ save__phasing_MIR.FOM _item_description.description ; The mean value of the figure of merit m for all reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.FOM' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.FOM_acentric _item_description.description ; The mean value of the figure of merit m for the acentric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.FOM_acentric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.FOM_centric _item_description.description ; The mean value of the figure of merit m for the centric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.FOM_centric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.method _item_description.description ; A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MIR phasing program. ; _item.name '_phasing_MIR.method' _item.category_id phasing_MIR _item.mandatory_code no _item_type.code text save_ save__phasing_MIR.reflns _item_description.description ; The total number of reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_acentric _item_description.description ; The number of acentric reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns_acentric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_centric _item_description.description ; The number of centric reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns_centric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_criterion _item_description.description ; Criterion used to limit the reflections used in the phasing calculations. ; _item.name '_phasing_MIR.reflns_criterion' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_criteria' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code text _item_examples.case '> 4 \s(I)' save_ ##################### ## PHASING_MIR_DER ## ##################### save_phasing_MIR_der _category.description ; Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via _phasing_MIR_der.der_set_id and _phasing_MIR_der.native_set_id. ; _category.id phasing_MIR_der _category.mandatory_code no _category_key.name '_phasing_MIR_der.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. ; ; loop_ _phasing_MIR_der.id _phasing_MIR_der.number_of_sites _phasing_MIR_der.details KAu(CN)2 3 'major site interpreted in difference Patterson' K2HgI4 6 'sites found in cross-difference Fourier' K3IrCl6 2 'sites found in cross-difference Fourier' All 11 'data for all three derivatives combined' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data used for this derivative. This is called the highest resolution. ; _item.name '_phasing_MIR_der.d_res_high' _item.category_id phasing_MIR_der _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data used for this derivative. This is called the lowest resolution. ; _item.name '_phasing_MIR_der.d_res_low' _item.category_id phasing_MIR_der _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der.der_set_id _item_description.description ; The data set that was treated as the derivative in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MIR_der.der_set_id' _item.mandatory_code yes save_ save__phasing_MIR_der.details _item_description.description ; A description of special aspects of this derivative, its data, its solution or its use in phasing. ; _item.name '_phasing_MIR_der.details' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code text save_ save__phasing_MIR_der.id _item_description.description ; The value of _phasing_MIR_der.id must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MIR_der.id' phasing_MIR_der yes '_phasing_MIR_der_refln.der_id' phasing_MIR_der_refln yes '_phasing_MIR_der_shell.der_id' phasing_MIR_der_shell yes '_phasing_MIR_der_site.der_id' phasing_MIR_der_site yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MIR_der_refln.der_id' '_phasing_MIR_der.id' '_phasing_MIR_der_shell.der_id' '_phasing_MIR_der.id' '_phasing_MIR_der_site.der_id' '_phasing_MIR_der.id' _item_type.code line loop_ _item_examples.case 'KAu(CN)2' 'K2HgI4_anom' 'K2HgI4_iso' save_ save__phasing_MIR_der.native_set_id _item_description.description ; The data set that was treated as the native in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MIR_der.native_set_id' _item.mandatory_code yes save_ save__phasing_MIR_der.number_of_sites _item_description.description ; The number of heavy-atom sites in this derivative. ; _item.name '_phasing_MIR_der.number_of_sites' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code int save_ save__phasing_MIR_der.power_acentric _item_description.description ; The mean phasing power P for acentric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of this derivative Fph~calc~ = the calculated structure-factor amplitude of this derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der.power_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_power_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.power_centric _item_description.description ; The mean phasing power P for centric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der.power_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_power_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_acentric _item_description.description ; Residual factor R~cullis,acen~ for acentric reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for acentric reflections, which is how it is used in this data item. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis,acen~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_anomalous _item_description.description ; Residual factor R~cullis,ano~ for anomalous reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for anomalous reflections, which is how it is used in this data item. This is tabulated for acentric terms. A value less than 1.0 means there is some contribution to the phasing from the anomalous data. sum |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| R~cullis,ano~ = ------------------------------------------------ sum|Fph+~obs~ - Fph-~obs~| Fph+~obs~ = the observed positive Friedel structure-factor amplitude for the derivative Fph-~obs~ = the observed negative Friedel structure-factor amplitude for the derivative Fh+~calc~ = the calculated positive Friedel structure-factor amplitude from the heavy-atom model Fh-~calc~ = the calculated negative Friedel structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_anomalous' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_anomalous' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_centric _item_description.description ; Residual factor R~cullis~ for centric reflections for this derivative. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.reflns_acentric _item_description.description ; The number of acentric reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_anomalous _item_description.description ; The number of anomalous reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_anomalous' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_anomalous' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_centric _item_description.description ; The number of centric reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_criteria _item_description.description ; Criteria used to limit the reflections used in the phasing calculations. ; _item.name '_phasing_MIR_der.reflns_criteria' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code text _item_examples.case '> 4 \s(I)' save_ ########################### ## PHASING_MIR_DER_REFLN ## ########################### save_phasing_MIR_der_refln _category.description ; Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_refln.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness. ; _category.id phasing_MIR_der_refln _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_der_refln.index_h' '_phasing_MIR_der_refln.index_k' '_phasing_MIR_der_refln.index_l' '_phasing_MIR_der_refln.der_id' '_phasing_MIR_der_refln.set_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the 6,1,25 reflection of an Hg/Pt derivative of protein NS1. ; ; _phasing_MIR_der_refln.index_h 6 _phasing_MIR_der_refln.index_k 1 _phasing_MIR_der_refln.index_l 25 _phasing_MIR_der_refln.der_id HGPT1 _phasing_MIR_der_refln.set_id 'NS1-96' _phasing_MIR_der_refln.F_calc_au 106.66 _phasing_MIR_der_refln.F_meas_au 204.67 _phasing_MIR_der_refln.F_meas_sigma 6.21 _phasing_MIR_der_refln.HL_A_iso -3.15 _phasing_MIR_der_refln.HL_B_iso -0.76 _phasing_MIR_der_refln.HL_C_iso 0.65 _phasing_MIR_der_refln.HL_D_iso 0.23 _phasing_MIR_der_refln.phase_calc 194.48 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der_refln.der_id _item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ; _item.name '_phasing_MIR_der_refln.der_id' _item.mandatory_code yes save_ save__phasing_MIR_der_refln.F_calc _item_description.description ; The calculated value of the structure factor for this derivative, in electrons. ; _item.name '_phasing_MIR_der_refln.F_calc' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_related.related_name '_phasing_MIR_der_refln.F_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__phasing_MIR_der_refln.F_calc_au _item_description.description ; The calculated value of the structure factor for this derivative, in arbitrary units. ; _item.name '_phasing_MIR_der_refln.F_calc_au' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_related.related_name '_phasing_MIR_der_refln.F_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__phasing_MIR_der_refln.F_meas _item_description.description ; The measured value of the structure factor for this derivative, in electrons. ; _item.name '_phasing_MIR_der_refln.F_meas' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas_sigma' associated_esd '_phasing_MIR_der_refln.F_meas_au' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code electrons save_ save__phasing_MIR_der_refln.F_meas_au _item_description.description ; The measured value of the structure factor for this derivative, in arbitrary units. ; _item.name '_phasing_MIR_der_refln.F_meas_au' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas_sigma_au' associated_esd '_phasing_MIR_der_refln.F_meas' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__phasing_MIR_der_refln.F_meas_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas, in electrons. ; _item.name '_phasing_MIR_der_refln.F_meas_sigma' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas' associated_value '_phasing_MIR_der_refln.F_meas_sigma_au' conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__phasing_MIR_der_refln.F_meas_sigma_au _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas_au, in arbitrary units. ; _item.name '_phasing_MIR_der_refln.F_meas_sigma_au' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas_au' associated_value '_phasing_MIR_der_refln.F_meas_sigma' conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__phasing_MIR_der_refln.HL_A_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * cos(alphah~calc~) A~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the calculated phase from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_A_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.HL_B_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * sin(alphah~calc~) B~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_B_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.HL_C_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection for this derivative. -Fp~obs~^2^ * [sin(alphah~calc~)^2^ - cos(alphah~calc~)^2^] C~iso~ = ------------------------------------ E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_C_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.HL_D_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection for this derivative. -2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^ * cos(alphah~calc~)^2^ D~iso~ = ---------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_D_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.index_h _item_description.description ; Miller index h for this reflection for this derivative. ; _item.name '_phasing_MIR_der_refln.index_h' _item.category_id phasing_MIR_der_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_MIR_der_refln.index_k' '_phasing_MIR_der_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_MIR_der_refln.index_k _item_description.description ; Miller index k for this reflection for this derivative. ; _item.name '_phasing_MIR_der_refln.index_k' _item.category_id phasing_MIR_der_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_MIR_der_refln.index_h' '_phasing_MIR_der_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_MIR_der_refln.index_l _item_description.description ; Miller index l for this reflection for this derivative. ; _item.name '_phasing_MIR_der_refln.index_l' _item.category_id phasing_MIR_der_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_MIR_der_refln.index_h' '_phasing_MIR_der_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_MIR_der_refln.phase_calc _item_description.description ; The calculated value of the structure-factor phase based on the heavy-atom model for this derivative in degrees. ; _item.name '_phasing_MIR_der_refln.phase_calc' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__phasing_MIR_der_refln.set_id _item_description.description ; This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MIR_der_refln.set_id' _item.mandatory_code yes save_ ########################### ## PHASING_MIR_DER_SHELL ## ########################### save_phasing_MIR_der_shell _category.description ; Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_shell.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) ; _category.id phasing_MIR_der_shell _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_der_shell.der_id' '_phasing_MIR_der_shell.d_res_low' '_phasing_MIR_der_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. ; ; loop_ _phasing_MIR_der_shell.der_id _phasing_MIR_der_shell.d_res_low _phasing_MIR_der_shell.d_res_high _phasing_MIR_der_shell.ha_ampl _phasing_MIR_der_shell.loc KAu(CN)2 15.0 8.3 54 26 KAu(CN)2 8.3 6.4 54 20 KAu(CN)2 6.4 5.2 50 20 KAu(CN)2 5.2 4.4 44 23 KAu(CN)2 4.4 3.8 39 23 KAu(CN)2 3.8 3.4 33 21 KAu(CN)2 3.4 3.0 28 17 KAu(CN)2 15.0 3.0 38 21 K2HgI4 15.0 8.3 149 87 K2HgI4 8.3 6.4 121 73 K2HgI4 6.4 5.2 95 61 K2HgI4 5.2 4.4 80 60 K2HgI4 4.4 3.8 73 63 K2HgI4 3.8 3.4 68 57 K2HgI4 3.4 3.0 63 46 K2HgI4 15.0 3.0 79 58 K3IrCl6 15.0 8.3 33 27 K3IrCl6 8.3 6.4 40 23 K3IrCl6 6.4 5.2 31 22 K3IrCl6 5.2 4.4 27 23 K3IrCl6 4.4 3.8 22 23 K3IrCl6 3.8 3.4 19 20 K3IrCl6 3.4 3.0 16 20 K3IrCl6 15.0 3.0 23 21 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der_shell.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the highest resolution. ; _item.name '_phasing_MIR_der_shell.d_res_high' _item.category_id phasing_MIR_der_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_shell.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the lowest resolution. ; _item.name '_phasing_MIR_der_shell.d_res_low' _item.category_id phasing_MIR_der_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_shell.der_id _item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ; _item.name '_phasing_MIR_der_shell.der_id' _item.mandatory_code yes save_ save__phasing_MIR_der_shell.fom _item_description.description ; The mean value of the figure of merit m for reflections for this derivative in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_der_shell.fom' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.ha_ampl _item_description.description ; The mean heavy-atom amplitude for reflections for this derivative in this shell. ; _item.name '_phasing_MIR_der_shell.ha_ampl' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.loc _item_description.description ; The mean lack-of-closure error loc for reflections for this derivative in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections ; _item.name '_phasing_MIR_der_shell.loc' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.phase _item_description.description ; The mean of the phase values for reflections for this derivative in this shell. ; _item.name '_phasing_MIR_der_shell.phase' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_shell.power _item_description.description ; The mean phasing power P for reflections for this derivative in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der_shell.power' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.R_cullis _item_description.description ; Residual factor R~cullis~ for centric reflections for this derivative in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der_shell.R_cullis' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.R_kraut _item_description.description ; Residual factor R~kraut~ for general reflections for this derivative in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. ; _item.name '_phasing_MIR_der_shell.R_kraut' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.reflns _item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_der_shell.reflns' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ ########################## ## PHASING_MIR_DER_SITE ## ########################## save_phasing_MIR_der_site _category.description ; Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_site.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) ; _category.id phasing_MIR_der_site _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_der_site.der_id' '_phasing_MIR_der_site.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with occupancies converted from electrons to fractional. ; ; loop_ _phasing_MIR_der_site.der_id _phasing_MIR_der_site.id _phasing_MIR_der_site.atom_type_symbol _phasing_MIR_der_site.occupancy _phasing_MIR_der_site.fract_x _phasing_MIR_der_site.fract_y _phasing_MIR_der_site.fract_z _phasing_MIR_der_site.B_iso KAu(CN)2 1 Au 0.40 0.082 0.266 0.615 33.0 KAu(CN)2 2 Au 0.03 0.607 0.217 0.816 25.9 KAu(CN)2 3 Au 0.02 0.263 0.782 0.906 15.7 K2HgI4 1 Hg 0.63 0.048 0.286 0.636 33.7 K2HgI4 2 Hg 0.34 0.913 0.768 0.889 36.7 K2HgI4 3 Hg 0.23 0.974 0.455 0.974 24.2 K2HgI4 4 Hg 0.28 0.903 0.836 0.859 14.7 K2HgI4 5 Hg 0.07 0.489 0.200 0.885 6.4 K2HgI4 6 Hg 0.07 0.162 0.799 0.889 32.9 K3IrCl6 1 Ir 0.26 0.209 0.739 0.758 40.8 K3IrCl6 2 Ir 0.05 0.279 0.613 0.752 24.9 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der_site.atom_type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. The scattering factors referenced via this data item should be those used in the refinement of the heavy-atom data; in some cases this is the scattering factor for the single heavy atom, in other cases these are the scattering factors for an atomic cluster. ; _item.name '_phasing_MIR_der_site.atom_type_symbol' _item.mandatory_code yes save_ save__phasing_MIR_der_site.B_iso _item_description.description ; Isotropic displacement parameter for this heavy-atom site in this derivative. ; _item.name '_phasing_MIR_der_site.B_iso' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_related.related_name '_phasing_MIR_der_site.B_iso_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.B_iso_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.B_iso. ; _item.name '_phasing_MIR_der_site.B_iso_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.B_iso' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_x _item_description.description ; The x coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_phasing_MIR_der_site.Cartn_x' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_y' '_phasing_MIR_der_site.Cartn_z' _item_related.related_name '_phasing_MIR_der_site.Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_x. ; _item.name '_phasing_MIR_der_site.Cartn_x_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_y_esd' '_phasing_MIR_der_site.Cartn_z_esd' _item_related.related_name '_phasing_MIR_der_site.Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_y _item_description.description ; The y coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_phasing_MIR_der_site.Cartn_y' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x' '_phasing_MIR_der_site.Cartn_z' _item_related.related_name '_phasing_MIR_der_site.Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_y. ; _item.name '_phasing_MIR_der_site.Cartn_y_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x_esd' '_phasing_MIR_der_site.Cartn_z_esd' _item_related.related_name '_phasing_MIR_der_site.Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_z _item_description.description ; The z coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_phasing_MIR_der_site.Cartn_z' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x' '_phasing_MIR_der_site.Cartn_y' _item_related.related_name '_phasing_MIR_der_site.Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_z. ; _item.name '_phasing_MIR_der_site.Cartn_z_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x_esd' '_phasing_MIR_der_site.Cartn_y_esd' _item_related.related_name '_phasing_MIR_der_site.Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.der_id _item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ; _item.name '_phasing_MIR_der_site.der_id' _item.mandatory_code yes save_ save__phasing_MIR_der_site.details _item_description.description ; A description of special aspects of the derivative site. ; _item.name '_phasing_MIR_der_site.details' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'binds to His 117' 'minor site obtained from difference Fourier' 'same as site 2 in the K2HgI4 derivative' save_ save__phasing_MIR_der_site.fract_x _item_description.description ; The x coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_a. ; _item.name '_phasing_MIR_der_site.fract_x' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_y' '_phasing_MIR_der_site.fract_z' _item_related.related_name '_phasing_MIR_der_site.fract_x_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.fract_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_x. ; _item.name '_phasing_MIR_der_site.fract_x_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_y_esd' '_phasing_MIR_der_site.fract_z_esd' _item_related.related_name '_phasing_MIR_der_site.fract_x' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__phasing_MIR_der_site.fract_y _item_description.description ; The y coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_b. ; _item.name '_phasing_MIR_der_site.fract_y' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x' '_phasing_MIR_der_site.fract_z' _item_related.related_name '_phasing_MIR_der_site.fract_y_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.fract_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_y. ; _item.name '_phasing_MIR_der_site.fract_y_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x_esd' '_phasing_MIR_der_site.fract_z_esd' _item_related.related_name '_phasing_MIR_der_site.fract_y' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__phasing_MIR_der_site.fract_z _item_description.description ; The z coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_c. ; _item.name '_phasing_MIR_der_site.fract_z' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x' '_phasing_MIR_der_site.fract_y' _item_related.related_name '_phasing_MIR_der_site.fract_z_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.fract_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_z. ; _item.name '_phasing_MIR_der_site.fract_z_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x_esd' '_phasing_MIR_der_site.fract_y_esd' _item_related.related_name '_phasing_MIR_der_site.fract_z' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__phasing_MIR_der_site.id _item_description.description ; The value of _phasing_MIR_der_site.id must uniquely identify each site in each derivative in the PHASING_MIR_DER_SITE list. The atom identifiers need not be unique over all sites in all derivatives; they need only be unique for each site in each derivative. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_phasing_MIR_der_site.id' _item.category_id phasing_MIR_der_site _item.mandatory_code yes _item_type.code code save_ save__phasing_MIR_der_site.occupancy _item_description.description ; The fraction of the atom type present at this heavy-atom site in a given derivative. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. ; _item.name '_phasing_MIR_der_site.occupancy' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_site.occupancy_anom _item_description.description ; The relative anomalous occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. ; _item.name '_phasing_MIR_der_site.occupancy_anom' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_anom_su' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.occupancy_anom_su _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.occupancy_anom. ; _item.name '_phasing_MIR_der_site.occupancy_anom_su' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom_esd' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 # _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_anom' _item_related.function_code associated_value _item_type.code float save_ save__phasing_MIR_der_site.occupancy_iso _item_description.description ; The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. ; _item.name '_phasing_MIR_der_site.occupancy_iso' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_iso_su' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.occupancy_iso_su _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.occupancy_iso. ; _item.name '_phasing_MIR_der_site.occupancy_iso_su' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso_esd' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 # _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_iso' _item_related.function_code associated_value _item_type.code float save_ ####################### ## PHASING_MIR_SHELL ## ####################### save_phasing_MIR_shell _category.description ; Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution. ; _category.id phasing_MIR_shell _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_shell.d_res_low' '_phasing_MIR_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. ; ; loop_ _phasing_MIR_shell.d_res_low _phasing_MIR_shell.d_res_high _phasing_MIR_shell.reflns _phasing_MIR_shell.FOM 15.0 8.3 80 0.69 8.3 6.4 184 0.73 6.4 5.2 288 0.72 5.2 4.4 406 0.65 4.4 3.8 554 0.54 3.8 3.4 730 0.53 3.4 3.0 939 0.50 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_shell.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. ; _item.name '_phasing_MIR_shell.d_res_high' _item.category_id phasing_MIR_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_shell.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. ; _item.name '_phasing_MIR_shell.d_res_low' _item.category_id phasing_MIR_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_shell.FOM _item_description.description ; The mean value of the figure of merit m for reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.FOM' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.FOM_acentric _item_description.description ; The mean value of the figure of merit m for acentric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.FOM_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.FOM_centric _item_description.description ; The mean value of the figure of merit m for centric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.FOM_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.loc _item_description.description ; The mean lack-of-closure error loc for reflections in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections ; _item.name '_phasing_MIR_shell.loc' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.mean_phase _item_description.description ; The mean of the phase values for all reflections in this shell. ; _item.name '_phasing_MIR_shell.mean_phase' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_shell.power _item_description.description ; The mean phasing power P for reflections in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_shell.power' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.R_cullis _item_description.description ; Residual factor R~cullis~ for centric reflections in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_shell.R_cullis' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.R_kraut _item_description.description ; Residual factor R~kraut~ for general reflections in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. ; _item.name '_phasing_MIR_shell.R_kraut' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.reflns _item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_acentric _item_description.description ; The number of acentric reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_anomalous _item_description.description ; The number of anomalous reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_anomalous' _item.category_id phasing_MIR_shell _item.mandatory_code no # _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_anomalous' # _item_aliases.dictionary ebi_extensions # _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_centric _item_description.description ; The number of centric reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ ################# ## PHASING_SET ## ################# save_phasing_set _category.description ; Data items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multiple-wavelength calculation. This category establishes identifiers for each data set and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature etc.). This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If all the possible experimental information for each data set (raw data sets, crystal growth conditions etc.) is to be archived, these data items should be recorded in a separate data block. ; _category.id phasing_set _category.mandatory_code no _category_key.name '_phasing_set.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for an Hg/Pt derivative of protein NS1. ; ; _phasing_set.id 'NS1-96' _phasing_set.cell_angle_alpha 90.0 _phasing_set.cell_angle_beta 90.0 _phasing_set.cell_angle_gamma 90.0 _phasing_set.cell_length_a 38.63 _phasing_set.cell_length_b 38.63 _phasing_set.cell_length_c 82.88 _phasing_set.radiation_wavelength 1.5145 _phasing_set.detector_type 'image plate' _phasing_set.detector_specific 'RXII' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_set.cell_angle_alpha _item_description.description ; Unit-cell angle alpha for this data set in degrees. ; _item.name '_phasing_set.cell_angle_alpha' _item.category_id phasing_set _item.mandatory_code no _item_default.value 90.0 loop_ _item_dependent.dependent_name '_phasing_set.cell_angle_beta' '_phasing_set.cell_angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_sub_category.id cell_angle _item_type.code float _item_units.code degrees save_ save__phasing_set.cell_angle_beta _item_description.description ; Unit-cell angle beta for this data set in degrees. ; _item.name '_phasing_set.cell_angle_beta' _item.category_id phasing_set _item.mandatory_code no _item_default.value 90.0 loop_ _item_dependent.dependent_name '_phasing_set.cell_angle_alpha' '_phasing_set.cell_angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_sub_category.id cell_angle _item_type.code float _item_units.code degrees save_ save__phasing_set.cell_angle_gamma _item_description.description ; Unit-cell angle gamma for this data set in degrees. ; _item.name '_phasing_set.cell_angle_gamma' _item.category_id phasing_set _item.mandatory_code no _item_default.value 90.0 loop_ _item_dependent.dependent_name '_phasing_set.cell_angle_alpha' '_phasing_set.cell_angle_beta' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_sub_category.id cell_angle _item_type.code float _item_units.code degrees save_ save__phasing_set.cell_length_a _item_description.description ; Unit-cell length a for this data set in angstroms. ; _item.name '_phasing_set.cell_length_a' _item.category_id phasing_set _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_set.cell_length_b' '_phasing_set.cell_length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_sub_category.id cell_length _item_type.code float _item_units.code angstroms save_ save__phasing_set.cell_length_b _item_description.description ; Unit-cell length b for this data set in angstroms. ; _item.name '_phasing_set.cell_length_b' _item.category_id phasing_set _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_set.cell_length_a' '_phasing_set.cell_length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_sub_category.id cell_length _item_type.code float _item_units.code angstroms save_ save__phasing_set.cell_length_c _item_description.description ; Unit-cell length c for this data set in angstroms. ; _item.name '_phasing_set.cell_length_c' _item.category_id phasing_set _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_set.cell_length_a' '_phasing_set.cell_length_b' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_sub_category.id cell_length _item_type.code float _item_units.code angstroms save_ save__phasing_set.detector_specific _item_description.description ; The particular radiation detector. In general, this will be a manufacturer, description, model number or some combination of these. ; _item.name '_phasing_set.detector_specific' _item.category_id phasing_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Siemens model x' 'Kodak XG' 'MAR Research model y' save_ save__phasing_set.detector_type _item_description.description ; The general class of the radiation detector. ; _item.name '_phasing_set.detector_type' _item.category_id phasing_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'multiwire' 'imaging plate' 'CCD' 'film' save_ save__phasing_set.id _item_description.description ; The value of _phasing_set.id must uniquely identify a record in the PHASING_SET list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_set.id' phasing_set yes '_phasing_set_refln.set_id' phasing_set_refln yes '_phasing_MAD_set.set_id' phasing_MAD_set yes '_phasing_MIR_der.der_set_id' phasing_MIR_der yes '_phasing_MIR_der.native_set_id' phasing_MIR_der yes '_phasing_MIR_der_refln.set_id' phasing_MIR_der_refln yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_set_refln.set_id' '_phasing_set.id' '_phasing_MAD_set.set_id' '_phasing_set.id' '_phasing_MIR_der.der_set_id' '_phasing_set.id' '_phasing_MIR_der.native_set_id' '_phasing_set.id' '_phasing_MIR_der_refln.set_id' '_phasing_set.id' _item_type.code line loop_ _item_examples.case 'KAu(CN)2' 'K2HgI4' save_ save__phasing_set.radiation_source_specific _item_description.description ; The particular source of radiation. In general, this will be a manufacturer, description, or model number (or some combination of these) for laboratory sources and an institution name and beamline name for synchrotron sources. ; _item.name '_phasing_set.radiation_source_specific' _item.category_id phasing_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Rigaku RU200' 'Philips fine focus Mo' 'NSLS beamline X8C' save_ save__phasing_set.radiation_wavelength _item_description.description ; The mean wavelength of the radiation used to measure this data set. ; _item.name '_phasing_set.radiation_wavelength' _item.category_id phasing_set _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_set.temp _item_description.description ; The temperature in kelvins at which the data set was measured. ; _item.name '_phasing_set.temp' _item.category_id phasing_set _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code kelvins save_ ####################### ## PHASING_SET_REFLN ## ####################### save_phasing_set_refln _category.description ; Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; _phasing_set_refln.set_id indicates the data set to which a given record corresponds. ; _category.id phasing_set_refln _category.mandatory_code no loop_ _category_key.name '_phasing_set_refln.index_h' '_phasing_set_refln.index_k' '_phasing_set_refln.index_l' '_phasing_set_refln.set_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the 15,15,32 reflection of an Hg/Pt derivative of protein NS1. ; ; _phasing_set_refln.set_id 'NS1-96' _phasing_set_refln.index_h 15 _phasing_set_refln.index_k 15 _phasing_set_refln.index_l 32 _phasing_set_refln.F_meas_au 181.79 _phasing_set_refln.F_meas_sigma_au 3.72 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_set_refln.set_id _item_description.description ; This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_set_refln.set_id' _item.mandatory_code yes save_ save__phasing_set_refln.F_meas _item_description.description ; The measured value of the structure factor for this reflection in this data set in electrons. ; _item.name '_phasing_set_refln.F_meas' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas_sigma' associated_esd '_phasing_set_refln.F_meas_au' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code electrons save_ save__phasing_set_refln.F_meas_au _item_description.description ; The measured value of the structure factor for this reflection in this data set in arbitrary units. ; _item.name '_phasing_set_refln.F_meas_au' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas_sigma_au' associated_esd '_phasing_set_refln.F_meas' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__phasing_set_refln.F_meas_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_set_refln.F_meas in electrons. ; _item.name '_phasing_set_refln.F_meas_sigma' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas' associated_value '_phasing_set_refln.F_meas_sigma_au' conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__phasing_set_refln.F_meas_sigma_au _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_set_refln.F_meas_au in arbitrary units. ; _item.name '_phasing_set_refln.F_meas_sigma_au' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas_au' associated_value '_phasing_set_refln.F_meas_sigma' conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__phasing_set_refln.index_h _item_description.description ; Miller index h of this reflection in this data set. ; _item.name '_phasing_set_refln.index_h' _item.category_id phasing_set_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_set_refln.index_k' '_phasing_set_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_set_refln.index_k _item_description.description ; Miller index k of this reflection in this data set. ; _item.name '_phasing_set_refln.index_k' _item.category_id phasing_set_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_set_refln.index_h' '_phasing_set_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_set_refln.index_l _item_description.description ; Miller index l of this reflection in this data set. ; _item.name '_phasing_set_refln.index_l' _item.category_id phasing_set_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_set_refln.index_h' '_phasing_set_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ ########## ## PUBL ## ########## save_publ _category.description ; Data items in the PUBL category are used when submitting a manuscript for publication. ; _category.id publ _category.mandatory_code no _category_key.name '_publ.entry_id' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _publ.section_title ; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)- 1,3-oxazolidin-5-one ; _publ.section_abstract ; The oxazolidinone ring is a shallow envelope conformation with the tert-butyl and iso-butyl groups occupying trans-positions with respect to the ring. The angles at the N atom sum to 356.2\%, indicating a very small degree of pyramidalization at this atom. This is consistent with electron delocalization between the N atom and the carbonyl centre [N-C=O = 1.374(3)\%A]. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick, Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527]. ; ; _publ.section_title ; Hemiasterlin methyl ester ; _publ.section_title_footnote ; IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl- 2-methylamino-3-(N-methylbenzo[b]pyrrol- 3-yl)butanamido]-3,3-dimethyl-N-methyl- butanamido}-2-hexenoate. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_publ.entry_id' _item.mandatory_code yes save_ save__publ.contact_author _item_description.description ; The name and address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. It is preferable to use the separate data items _publ.contact_author_name and _publ.contact_author_address. ; _item.name '_publ.contact_author' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Professor George Ferguson Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 ; save_ save__publ.contact_author_address _item_description.description ; The address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. ; _item.name '_publ.contact_author_address' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 ; save_ save__publ.contact_author_email _item_description.description ; E-mail address in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; _item.name '_publ.contact_author_email' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'name@host.domain.country' 'uur5@banjo.bitnet' save_ save__publ.contact_author_fax _item_description.description ; Facsimile telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. ; _item.name '_publ.contact_author_fax' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477330' '12()349477330' save_ save__publ.contact_author_name _item_description.description ; The name of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. ; _item.name '_publ.contact_author_name' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Professor George Ferguson ; save_ save__publ.contact_author_phone _item_description.description ; Telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. ; _item.name '_publ.contact_author_phone' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477330' '12()349477330' '12(34)9477330x5543' save_ save__publ.contact_letter _item_description.description ; A letter submitted to the journal editor by the contact author. ; _item.name '_publ.contact_letter' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_letter' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.manuscript_creation _item_description.description ; A description of the word-processor package and computer used to create the word-processed manuscript stored as _publ.manuscript_processed. ; _item.name '_publ.manuscript_creation' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_creation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Tex file created by FrameMaker on a Sun 3/280' save_ save__publ.manuscript_processed _item_description.description ; The full manuscript of a paper (excluding possibly the figures and the tables) output in ASCII characters from a word processor. Information about the generation of this data item must be specified in the data item _publ.manuscript_creation. ; _item.name '_publ.manuscript_processed' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_processed' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.manuscript_text _item_description.description ; The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text. ; _item.name '_publ.manuscript_text' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_text' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.requested_category _item_description.description ; The category of paper submitted. For submission to Acta Crystallographica Section C or Acta Crystallographica Section E, ONLY the codes indicated for use with these journals should be used. ; _item.name '_publ.requested_category' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_requested_category' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value FA _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail FA 'Full article' FI 'Full submission - inorganic (Acta C)' FO 'Full submission - organic (Acta C)' FM 'Full submission - metal-organic (Acta C)' CI 'CIF-access paper - inorganic (Acta C) (no longer in use)' CO 'CIF-access paper - organic (Acta C) (no longer in use)' CM 'CIF-access paper - metal-organic (Acta C) (no longer in use)' EI 'Electronic submission - inorganic (Acta E)' EO 'Electronic submission - organic (Acta E)' EM 'Electronic submission - metal-organic (Acta E)' AD 'Addenda and Errata (Acta C, Acta E)' SC 'Short communication' save_ save__publ.requested_coeditor_name _item_description.description ; The name of the co-editor whom the authors would like to handle the submitted manuscript. ; _item.name '_publ.requested_coeditor_name' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_requested_coeditor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__publ.requested_journal _item_description.description ; The name of the journal to which the manuscript is being submitted. ; _item.name '_publ.requested_journal' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_requested_journal' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__publ.section_abstract _item_description.description ; The abstract section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_abstract' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_abstract' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_acknowledgements _item_description.description ; The acknowledgements section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_acknowledgements' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_acknowledgements' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_comment _item_description.description ; The comment section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_comment' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_comment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_discussion _item_description.description ; The discussion section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_discussion' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_discussion' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_experimental _item_description.description ; The experimental section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. The _publ.section_exptl_prep, _publ.section_exptl_solution and _publ.section_exptl_refinement items are preferred for separating the chemical preparation, structure solution and refinement aspects of the description of the experiment. ; _item.name '_publ.section_experimental' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_experimental' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_exptl_prep _item_description.description ; The experimental preparation section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_exptl_prep' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_prep' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_exptl_refinement _item_description.description ; The experimental refinement section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_exptl_refinement' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_refinement' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_exptl_solution _item_description.description ; The experimental solution section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_exptl_solution' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_solution' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_figure_captions _item_description.description ; The figure captions section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_figure_captions' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_figure_captions' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_introduction _item_description.description ; The introduction section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_introduction' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_introduction' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_references _item_description.description ; The references section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_references' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_references' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_synopsis _item_description.description ; The synopsis section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_synopsis' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_synopsis' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_table_legends _item_description.description ; The table legends section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_table_legends' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_table_legends' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_title _item_description.description ; The title of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_title' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_title_footnote _item_description.description ; The footnote to the title of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_title_footnote' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_title_footnote' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ################# ## PUBL_AUTHOR ## ################# save_publ_author _category.description ; Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication. ; _category.id publ_author _category.mandatory_code no _category_key.name '_publ_author.name' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _publ_author.name _publ_author.address 'Willis, Anthony C.' ; Research School of Chemistry Australian National University GPO Box 4 Canberra, A.C.T. Australia 2601 ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ_author.address _item_description.description ; The address of a publication author. If there is more than one author this is looped with _publ_author.name. ; _item.name '_publ_author.address' _item.category_id publ_author _item.mandatory_code no _item_aliases.alias_name '_publ_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__publ_author.email _item_description.description ; The e-mail address of a publication author. If there is more than one author, this will be looped with _publ_author.name. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; _item.name '_publ_author.email' _item.category_id publ_author _item.mandatory_code no _item_aliases.alias_name '_publ_author_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.3.1 _item_type.code text loop_ _item_examples.case name@host.domain.country bm@iucr.org save_ save__publ_author.footnote _item_description.description ; A footnote accompanying an author's name in the list of authors of a paper. Typically indicates sabbatical address, additional affiliations or date of decease. ; _item.name '_publ_author.footnote' _item.category_id publ_author _item.mandatory_code no _item_aliases.alias_name '_publ_author_footnote' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'On leave from U. Western Australia' 'Also at Department of Biophysics' save_ save__publ_author.name _item_description.description ; The name of a publication author. If there are multiple authors this will be looped with _publ_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first names or initials. ; _item.name '_publ_author.name' _item.category_id publ_author _item.mandatory_code yes _item_aliases.alias_name '_publ_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' 'O'Neil, F.K.' 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ ############### ## PUBL_BODY ## ############### save_publ_body _category.description ; Data items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors. ; _category.id publ_body _category.mandatory_code no loop_ _category_key.name '_publ_body.element' '_publ_body.label' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by R. Restori & D. Schwarzenbach [Acta Cryst. (1996), A52, 369-378]. ; ; loop_ _publ_body.element _publ_body.label _publ_body.title _publ_body.format _publ_body.contents section 1 Introduction cif ; X-ray diffraction from a crystalline material provides information on the thermally and spatially averaged electron density in the crystal... ; section 2 Theory tex ; In the rigid-atom approximation, the dynamic electron density of an atom is described by the convolution product of the static atomic density and a probability density function, $\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$ ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens [Acta Cryst. (1996), A52, 397-407]. ; ; loop_ _publ_body.element _publ_body.label _publ_body.title _publ_body.contents section 3 ; The two-channel method for retrieval of the deformation electron density ; . subsection 3.1 'The two-channel entropy S[\D\r(r)]' ; As the wide dynamic range involved in the total electron density... ; subsection 3.2 'Uniform vs informative prior model densities' . subsubsection 3.2.1 'Use of uniform models' ; Straightforward algebra leads to expressions analogous to... ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ_body.contents _item_description.description ; A text section of a paper. ; _item.name '_publ_body.contents' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_contents' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ_body.element _item_description.description ; The functional role of the associated text section. ; _item.name '_publ_body.element' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_element' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_enumeration.value 'section' 'subsection' 'subsubsection' 'appendix' 'footnote' save_ save__publ_body.format _item_description.description ; Code indicating the appropriate typesetting conventions for accented characters and special symbols in the text section. ; _item.name '_publ_body.format' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_format' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail ascii 'no coding for special symbols' cif 'CIF convention' latex 'LaTeX' sgml 'SGML (ISO 8879)' tex 'TeX' troff 'troff or nroff' save_ save__publ_body.label _item_description.description ; Code identifying the section of text. ; _item.name '_publ_body.label' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_label' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_examples.case '1' '1.1' '2.1.3' save_ save__publ_body.title _item_description.description ; Title of the associated section of text. ; _item.name '_publ_body.title' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ########################## ## PUBL_MANUSCRIPT_INCL ## ########################## save_publ_manuscript_incl _category.description ; Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software. ; _category.id publ_manuscript_incl _category.mandatory_code no _category_key.name '_publ_manuscript_incl.entry_id' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; _publ_manuscript_incl.entry_id 'EXAMHYPO' loop_ _publ_manuscript_incl.extra_item _publ_manuscript_incl.extra_info _publ_manuscript_incl.extra_defn '_atom_site.symmetry_multiplicity' 'to emphasise special sites' yes '_chemical.compound_source' 'rare material, unusual source' yes '_reflns.d_resolution_high' 'limited data is a problem here' yes '_crystal.magnetic_permeability' 'unusual value for this material' no ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ_manuscript_incl.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_publ_manuscript_incl.entry_id' _item.mandatory_code yes save_ save__publ_manuscript_incl.extra_defn _item_description.description ; Flags whether the corresponding data item marked for inclusion in a journal request list is a standard CIF definition or not. ; _item.name '_publ_manuscript_incl.extra_defn' _item.category_id publ_manuscript_incl _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_defn' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail no 'not a standard CIF data name' n 'abbreviation for "no"' yes 'a standard CIF data name' y 'abbreviation for "yes"' save_ save__publ_manuscript_incl.extra_info _item_description.description ; A short note indicating the reason why the author wishes the corresponding data item marked for inclusion in the journal request list to be published. ; _item.name '_publ_manuscript_incl.extra_info' _item.category_id publ_manuscript_incl _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_info' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'to emphasise very special sites' 'rare material from unusual source' 'the limited data is a problem here' 'a new data quantity needed here' save_ save__publ_manuscript_incl.extra_item _item_description.description ; Specifies the inclusion of specific data into a manuscript which are not normally requested by the journal. The values of this item are the extra data names (which MUST be enclosed in single quotes) that will be added to the journal request list. ; _item.name '_publ_manuscript_incl.extra_item' _item.category_id publ_manuscript_incl _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_item' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '_atom_site.symmetry_multiplicity' '_chemical.compound_source' '_reflns.d_resolution_high' '_crystal.magnetic_permeability' save_ ############ ## REFINE ## ############ save_refine _category.description ; Data items in the REFINE category record details about the structure-refinement parameters. ; _category.id refine _category.mandatory_code no _category_key.name '_refine.entry_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _refine.entry_id '5HVP' _refine.ls_number_reflns_obs 12901 _refine.ls_number_restraints 6609 _refine.ls_number_parameters 7032 _refine.ls_R_Factor_obs 0.176 _refine.ls_weighting_scheme calc _refine.ls_weighting_details ; Sigdel model of Konnert-Hendrickson: Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = -150.0 at beginning of refinement Afsig = 15.5, Bfsig = -50.0 at end of refinement ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _refine.details sfls:_F_calc_weight_full_matrix _refine.ls_structure_factor_coef F _refine.ls_matrix_type full _refine.ls_weighting_scheme calc _refine.ls_weighting_details 'w=1/(\s^2^(F)+0.0004F^2^)' _refine.ls_hydrogen_treatment 'refxyz except H332B noref' _refine.ls_extinction_method Zachariasen _refine.ls_extinction_coef 3514 _refine.ls_extinction_expression ; Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard. _refine.ls_abs_structure_details ; The absolute configuration was assigned to agree with the known chirality at C3 arising from its precursor l-leucine. ; _refine.ls_abs_structure_Flack 0 _refine.ls_number_reflns_obs 1408 _refine.ls_number_parameters 272 _refine.ls_number_restraints 0 _refine.ls_number_constraints 0 _refine.ls_R_factor_all .038 _refine.ls_R_factor_obs .034 _refine.ls_wR_factor_all .044 _refine.ls_wR_factor_obs .042 _refine.ls_goodness_of_fit_all 1.462 _refine.ls_goodness_of_fit_obs 1.515 _refine.ls_shift_over_esd_max .535 _refine.ls_shift_over_esd_mean .044 _refine.diff_density_min -.108 _refine.diff_density_max .131 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine.aniso_B[1][1] _item_description.description ; The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[1][1]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[1][2] _item_description.description ; The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[1][2]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[1][3] _item_description.description ; The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[1][3]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[2][2] _item_description.description ; The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[2][2]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[2][3] _item_description.description ; The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[2][3]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[3][3] _item_description.description ; The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[3][3]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.B_iso_max _item_description.description ; The maximum isotropic displacement parameter (B value) found in the coordinate set. ; _item.name '_refine.B_iso_max' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__refine.B_iso_mean _item_description.description ; The mean isotropic displacement parameter (B value) for the coordinate set. ; _item.name '_refine.B_iso_mean' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__refine.B_iso_min _item_description.description ; The minimum isotropic displacement parameter (B value) found in the coordinate set. ; _item.name '_refine.B_iso_min' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__refine.correlation_coeff_Fo_to_Fc _item_description.description ; The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections included in the refinement ; _item.name '_refine.correlation_coeff_Fo_to_Fc' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.correlation_coeff_Fo_to_Fc_free _item_description.description ; The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections not included in the refinement (free reflections) ; _item.name '_refine.correlation_coeff_Fo_to_Fc_free' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc_free' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.details _item_description.description ; Description of special aspects of the refinement process. ; _item.name '_refine.details' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__refine.diff_density_max _item_description.description ; The maximum value of the electron density in the final difference Fourier map. ; _item.name '_refine.diff_density_max' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.diff_density_max_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_max_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.diff_density_max. ; _item.name '_refine.diff_density_max_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.diff_density_max' _item_related.function_code associated_value _item_type.code float _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_min _item_description.description ; The minimum value of the electron density in the final difference Fourier map. ; _item.name '_refine.diff_density_min' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.diff_density_min_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_min_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.diff_density_min. ; _item.name '_refine.diff_density_min_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.diff_density_min' _item_related.function_code associated_value _item_type.code float _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_rms _item_description.description ; The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels. ; _item.name '_refine.diff_density_rms' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_rms' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.diff_density_rms_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_rms_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.diff_density_rms. ; _item.name '_refine.diff_density_rms_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.diff_density_rms' _item_related.function_code associated_value _item_type.code float _item_units.code electrons_per_angstroms_cubed save_ save__refine.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_refine.entry_id' _item.mandatory_code yes save_ save__refine.ls_abs_structure_details _item_description.description ; The nature of the absolute structure and how it was determined. For example, this may describe the Friedel pairs used. ; _item.name '_refine.ls_abs_structure_details' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__refine.ls_abs_structure_Flack _item_description.description ; The measure of absolute structure (enantiomorph or polarity) as defined by Flack (1983). For centrosymmetric structures, the only permitted value, if the data name is present, is 'inapplicable', represented by '.' . For noncentrosymmetric structures the value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [0.0:1.0] is correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. ; _item.name '_refine.ls_abs_structure_Flack' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_Flack' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_related.related_name '_refine.ls_abs_structure_Flack_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_abs_structure_Flack_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_abs_structure_Flack. ; _item.name '_refine.ls_abs_structure_Flack_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_abs_structure_Flack' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_abs_structure_Rogers _item_description.description ; The measure of absolute structure (enantiomorph or polarity) as defined by Rogers. The value must lie in the 99.97% Gaussian confidence interval -1 -3u =< \h =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [-1.0, 1.0] is correctly interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u). Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. ; _item.name '_refine.ls_abs_structure_Rogers' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_Rogers' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 -1.0 -1.0 -1.0 _item_related.related_name '_refine.ls_abs_structure_Rogers_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_abs_structure_Rogers_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_abs_structure_Rogers. ; _item.name '_refine.ls_abs_structure_Rogers_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_abs_structure_Rogers' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_d_res_high _item_description.description ; The smallest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the highest resolution. ; _item.name '_refine.ls_d_res_high' _item.category_id refine _item.mandatory_code yes _item_aliases.alias_name '_refine_ls_d_res_high' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine.ls_d_res_low _item_description.description ; The largest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the lowest resolution. ; _item.name '_refine.ls_d_res_low' _item.category_id refine _item.mandatory_code yes _item_aliases.alias_name '_refine_ls_d_res_low' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine.ls_extinction_coef _item_description.description ; The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of _refine.ls_extinction_expression and _refine.ls_extinction_method. For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-47, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. ; _item.name '_refine.ls_extinction_coef' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_coef' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.ls_extinction_coef_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_examples.case 3472 _item_examples.detail 'Zachariasen coefficient r* = 0.347 E04' save_ save__refine.ls_extinction_coef_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_extinction_coef. ; _item.name '_refine.ls_extinction_coef_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_extinction_coef' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_extinction_expression _item_description.description ; A description of or reference to the extinction-correction equation used to apply the data item _refine.ls_extinction_coef. This information must be sufficient to reproduce the extinction-correction factors applied to the structure factors. ; _item.name '_refine.ls_extinction_expression' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_expression' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22), p.292. Copenhagen: Munksgaard. ; save_ save__refine.ls_extinction_method _item_description.description ; A description of the extinction-correction method applied. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method, it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian' and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied, the multiple coefficients cannot be contained in *_extinction_coef and must be listed in _refine.details. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. ; _item.name '_refine.ls_extinction_method' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value Zachariasen _item_type.code text _item_examples.case 'B-C type 2 Gaussian isotropic' save_ save__refine.ls_goodness_of_fit_all _item_description.description ; The least-squares goodness-of-fit parameter S for all data after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of _refine.ls_restrained_S_all. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_goodness_of_fit_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_all_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_goodness_of_fit_all_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_goodness_of_fit_all. ; _item.name '_refine.ls_goodness_of_fit_all_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_all' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_goodness_of_fit_obs _item_description.description ; The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see _reflns.observed_criterion) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of _refine.ls_restrained_S_obs. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_goodness_of_fit_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_obs_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_goodness_of_fit_obs_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_goodness_of_fit_obs. ; _item.name '_refine.ls_goodness_of_fit_obs_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_obs' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_hydrogen_treatment _item_description.description ; Treatment of hydrogen atoms in the least-squares refinement. ; _item.name '_refine.ls_hydrogen_treatment' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_hydrogen_treatment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value undef _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail refall 'refined all H-atom parameters' refxyz 'refined H-atom coordinates only' refU 'refined H-atom U's only' noref 'no refinement of H-atom parameters' constr 'H-atom parameters constrained' mixed 'some constrained, some independent' undef 'H-atom parameters not defined' save_ save__refine.ls_matrix_type _item_description.description ; Type of matrix used to accumulate the least-squares derivatives. ; _item.name '_refine.ls_matrix_type' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_matrix_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value full _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail full 'full' fullcycle 'full with fixed elements per cycle' atomblock 'block diagonal per atom' userblock 'user-defined blocks' diagonal 'diagonal elements only' sparse 'selected elements only' save_ save__refine.ls_number_constraints _item_description.description ; The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site.refinement_flags. A general description of constraints may appear in _refine.details. ; _item.name '_refine.ls_number_constraints' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_constraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_parameters _item_description.description ; The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. ; _item.name '_refine.ls_number_parameters' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_parameters' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_all _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. ; _item.name '_refine.ls_number_reflns_all' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. ; _item.name '_refine.ls_number_reflns_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_reflns' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine.ls_number_reflns_R_free' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_R_work _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine.ls_number_reflns_R_work' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_restraints _item_description.description ; The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags. A general description of refinement constraints may appear in _refine.details. ; _item.name '_refine.ls_number_restraints' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_restraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_percent_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. ; _item.name '_refine.ls_percent_reflns_obs' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_percent_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. ; _item.name '_refine.ls_percent_reflns_R_free' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_R_factor_all _item_description.description ; Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_factor_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_wR_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_R_factor_obs _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_factor_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_wR_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_R_factor_R_free _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_R_free' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_wR_factor_R_free' alternate '_refine.ls_R_factor_R_free_error' associated_error _item_type.code float save_ save__refine.ls_R_factor_R_free_error _item_description.description ; The estimated error in _refine.ls_R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details. ; _item.name '_refine.ls_R_factor_R_free_error' _item.category_id refine _item.mandatory_code no _item_related.related_name '_refine.ls_R_factor_R_free' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_R_factor_R_free_error_details _item_description.description ; Special aspects of the method used to estimated the error in _refine.ls_R_factor_R_free. ; _item.name '_refine.ls_R_factor_R_free_error_details' _item.category_id refine _item.mandatory_code no _item_type.code text save_ save__refine.ls_R_factor_R_work _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_R_work' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_wR_factor_R_work' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_R_Fsqd_factor_obs _item_description.description ; Residual factor R(Fsqd) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the squares of the observed and calculated structure-factor amplitudes. sum|F~obs~^2^ - F~calc~^2^| R(Fsqd) = --------------------------- sum|F~obs~^2^| F~obs~^2^ = squares of the observed structure-factor amplitudes F~calc~^2^ = squares of the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_Fsqd_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_Fsqd_factor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_R_I_factor_obs _item_description.description ; Residual factor R(I) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the estimated reflection intensities. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum|I~obs~ - I~calc~| R(I) = --------------------- sum|I~obs~| I~obs~ = the net observed intensities I~calc~ = the net calculated intensities sum is taken over the specified reflections ; _item.name '_refine.ls_R_I_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_I_factor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_redundancy_reflns_all _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine.ls_redundancy_reflns_all' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_redundancy_reflns_obs _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine.ls_redundancy_reflns_obs' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_restrained_S_all _item_description.description ; The least-squares goodness-of-fit parameter S' for all reflections after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_all. ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) N~restr~ = the number of restraints (see _refine.ls_number_restraints) N~param~ = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflections sumr is taken over the restraints ; _item.name '_refine.ls_restrained_S_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_restrained_S_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_restrained_S_obs _item_description.description ; The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see _reflns.observed_criterion) after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_obs. ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) N~restr~ = the number of restraints (see _refine.ls_number_restraints) N~param~ = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflections sumr is taken over the restraints ; _item.name '_refine.ls_restrained_S_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_restrained_S_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_shift_over_esd_max _item_description.description ; The largest ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). ; _item.name '_refine.ls_shift_over_esd_max' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_shift/esd_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_shift_over_esd_mean _item_description.description ; The average ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). ; _item.name '_refine.ls_shift_over_esd_mean' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_shift/esd_mean' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_structure_factor_coef _item_description.description ; Structure-factor coefficient |F|, F^2^ or I used in the least- squares refinement process. ; _item.name '_refine.ls_structure_factor_coef' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_structure_factor_coef' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value F _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail F 'structure-factor magnitude' Fsqd 'structure factor squared' Inet 'net intensity' save_ save__refine.ls_weighting_details _item_description.description ; A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of _refine.ls_weighting_scheme is specified as 'calc'. ; _item.name '_refine.ls_weighting_details' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_weighting_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. ; save_ save__refine.ls_weighting_scheme _item_description.description ; The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see _refine.ls_weighting_details for a preferred approach). ; _item.name '_refine.ls_weighting_scheme' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_weighting_scheme' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value sigma _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sigma 'based on measured e.s.d.'s' unit 'unit or no weights applied' calc 'calculated weights applied' save_ save__refine.ls_wR_factor_all _item_description.description ; Weighted residual factor wR for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_wR_factor_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_wR_factor_obs _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_wR_factor_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_wR_factor_R_free _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_R_free' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_R_free' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_wR_factor_R_work _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_R_work' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_R_work' _item_related.function_code alternate _item_type.code float save_ save__refine.occupancy_max _item_description.description ; The maximum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_max' _item.category_id refine _item.mandatory_code no # _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.occupancy_min _item_description.description ; The minimum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_min' _item.category_id refine _item.mandatory_code no # _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.overall_SU_B _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on a maximum-likelihood residual. The overall standard uncertainty (sigma~B~)^2 gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma~B~)^2 = 8 ---------------------------------------------- sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^4} SUM_AS = (sigma_A)^2/Sigma^2 N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2] E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_B' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_B' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_SU_ML _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~X~)^2 gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N_a (sigma~X~)^2 = ----------------------------------------------------- 8 pi^2 sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^2} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon [1-{sigma_A)^2] E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector epsilon = multiplicity of the diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_ML' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_ML' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_SU_R_Cruickshank_DPI _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3) (N_o-N_p) N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_value = conventional crystallographic R value D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_R_Cruickshank_DPI' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_R_Cruickshanks_DPI' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_SU_R_free _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the free R value. The overall standard uncertainty gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3) N_o N_a = number of atoms N_o = number of reflections included in refinement R_free = conventional free crystallographic R value calculated using reflections not included in refinement D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_R_free' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_Rfree' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_FOM_free_R_set _item_description.description ; Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel functions of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2] sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. ; _item.name '_refine.overall_FOM_free_R_set' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_FOM_free_Rset' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_FOM_work_R_set _item_description.description ; Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel functions of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2] sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. ; _item.name '_refine.overall_FOM_work_R_set' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_FOM_work_Rset' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.solvent_model_details _item_description.description ; Special aspects of the solvent model used during refinement. ; _item.name '_refine.solvent_model_details' _item.category_id refine _item.mandatory_code no _item_type.code text save_ save__refine.solvent_model_param_bsol _item_description.description ; The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms. This is one of the two parameters (the other is _refine.solvent_model_param_ksol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. ; _item.name '_refine.solvent_model_param_bsol' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.solvent_model_param_ksol _item_description.description ; The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute. This is one of the two parameters (the other is _refine.solvent_model_param_bsol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. ; _item.name '_refine.solvent_model_param_ksol' _item.category_id refine _item.mandatory_code no _item_type.code float save_ #################### ## REFINE_ANALYZE ## #################### save_refine_analyze _category.description ; Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names. ; _category.id refine_analyze _category.mandatory_code no _category_key.name '_refine_analyze.entry_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_analyze.entry_id _refine_analyze.Luzzati_coordinate_error_obs _refine_analyze.Luzzati_d_res_low_obs 5HVP 0.056 2.51 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_analyze.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_refine_analyze.entry_id' _item.category_id refine_analyze _item.mandatory_code yes save_ save__refine_analyze.Luzzati_coordinate_error_free _item_description.description ; The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_coordinate_error_free' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_coordinate_error_obs _item_description.description ; The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_coordinate_error_obs' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_d_res_low_free _item_description.description ; The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_d_res_low_free' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_d_res_low_obs _item_description.description ; The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_d_res_low_obs' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_sigma_a_free _item_description.description ; The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set during refinement. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_free_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_free' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_sigma_a_free_details _item_description.description ; Details of the estimation of sigma~a~ for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_free_details' _item.category_id refine_analyze _item.mandatory_code no _item_type.code text save_ save__refine_analyze.Luzzati_sigma_a_obs _item_description.description ; The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_obs_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_obs' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_sigma_a_obs_details _item_description.description ; Special aspects of the estimation of sigma~a~ for the reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_obs_details' _item.category_id refine_analyze _item.mandatory_code no _item_type.code text save_ save__refine_analyze.number_disordered_residues _item_description.description ; The number of discretely disordered residues in the refined model. ; _item.name '_refine_analyze.number_disordered_residues' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float save_ save__refine_analyze.occupancy_sum_hydrogen _item_description.description ; The sum of the occupancies of the hydrogen atoms in the refined model. ; _item.name '_refine_analyze.occupancy_sum_hydrogen' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float save_ save__refine_analyze.occupancy_sum_non_hydrogen _item_description.description ; The sum of the occupancies of the non-hydrogen atoms in the refined model. ; _item.name '_refine_analyze.occupancy_sum_non_hydrogen' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float save_ save__refine_analyze.RG_d_res_high _item_description.description ; The value of the high-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in _refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_d_res_high' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_high' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_analyze.RG_d_res_low _item_description.description ; The value of the low-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in _refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_d_res_low' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_low' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_analyze.RG_free _item_description.description ; The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_free' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_free' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_analyze.RG_work _item_description.description ; The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low and for those reflections included in the working set when a free R set of reflections is omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_work' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_work' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_analyze.RG_free_work_ratio _item_description.description ; The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in the data and the model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement, the ratio of RGfree to RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters according to sqrt[(f + m) / (f - m) ] where f = the number of included structure amplitudes and target distances, and m = the number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in the refinement, the RG ratio requires a term for the contribution to the minimized residual at convergence, D~restr~, due to those restraints: D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i] where r is the number of geometrical, displacement-parameter and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + D~restr~))/ (f - (m - r + D~restr~)) ] There is no data name for the expected value of RGfree/RGwork yet. Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547-557. ; _item.name '_refine_analyze.RG_free_work_ratio' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_work_free_ratio' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################## ## REFINE_B_ISO ## ################## save_refine_B_iso _category.description ; Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement. ; _category.id refine_B_iso _category.mandatory_code no _category_key.name '_refine_B_iso.class' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_B_iso.class _refine_B_iso.treatment 'protein' isotropic 'solvent' isotropic 'inhibitor' isotropic ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_B_iso.class _item_description.description ; A class of atoms treated similarly for isotropic B-factor (displacement-parameter) refinement. ; _item.name '_refine_B_iso.class' _item.category_id refine_B_iso _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'all' 'protein' 'solvent' 'sugar-phosphate backbone' save_ save__refine_B_iso.details _item_description.description ; A description of special aspects of the isotropic B-factor (displacement-parameter) refinement for the class of atoms described in _refine_B_iso.class. ; _item.name '_refine_B_iso.details' _item.category_id refine_B_iso _item.mandatory_code no _item_type.code text _item_examples.case ; The temperature factors of atoms in the side chain of Arg 92 were held fixed due to unstable behavior in refinement. ; save_ save__refine_B_iso.treatment _item_description.description ; The treatment of isotropic B-factor (displacement-parameter) refinement for a class of atoms defined in _refine_B_iso.class. ; _item.name '_refine_B_iso.treatment' _item.category_id refine_B_iso _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value fixed isotropic anisotropic save_ save__refine_B_iso.value _item_description.description ; The value of the isotropic B factor (displacement parameter) assigned to a class of atoms defined in _refine_B_iso.class. Meaningful only for atoms with fixed isotropic B factors. ; _item.name '_refine_B_iso.value' _item.category_id refine_B_iso _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ ############################### ## REFINE_FUNCTION_MINIMIZED ## ############################### save_refine_funct_minimized _category.description ; Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement. ; _category.id refine_funct_minimized _category.mandatory_code no _category_key.name '_refine_funct_minimized.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. ; ; loop_ _refine_funct_minimized.type _refine_funct_minimized.number_terms _refine_funct_minimized.residual 'sum(W*Delta(Amplitude)^2' 3009 1621.3 'sum(W*Delta(Plane+Rigid)^2' 85 56.68 'sum(W*Delta(Distance)^2' 1219 163.59 'sum(W*Delta(U-tempfactors)^2' 1192 69.338 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_funct_minimized.number_terms _item_description.description ; The number of observations in this term. For example, if the term is a residual of the X-ray intensities, this item would contain the number of reflections used in the refinement. ; _item.name '_refine_funct_minimized.number_terms' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.NumTerms' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_funct_minimized.residual _item_description.description ; The residual for this term of the function that was minimized during the refinement. ; _item.name '_refine_funct_minimized.residual' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.Residual' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_funct_minimized.type _item_description.description ; The type of the function being minimized. ; _item.name '_refine_funct_minimized.type' _item.category_id refine_funct_minimized _item.mandatory_code yes _item_aliases.alias_name '_ebi_refine_funct_minimized.type' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code line save_ save__refine_funct_minimized.weight _item_description.description ; The weight applied to this term of the function that was minimized during the refinement. ; _item.name '_refine_funct_minimized.weight' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.weight' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ ################# ## REFINE_HIST ## ################# save_refine_hist _category.description ; Data items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics. ; _category.id refine_hist _category.mandatory_code no _category_key.name '_refine_hist.cycle_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. ; ; _refine_hist.cycle_id C134 _refine_hist.d_res_high 1.85 _refine_hist.d_res_low 20.0 _refine_hist.number_atoms_solvent 217 _refine_hist.number_atoms_total 808 _refine_hist.number_reflns_all 6174 _refine_hist.number_reflns_obs 4886 _refine_hist.number_reflns_R_free 476 _refine_hist.number_reflns_R_work 4410 _refine_hist.R_factor_all .265 _refine_hist.R_factor_obs .195 _refine_hist.R_factor_R_free .274 _refine_hist.R_factor_R_work .160 _refine_hist.details ; Add majority of solvent molecules. B factors refined by group. Continued to remove misplaced water molecules. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_hist.cycle_id _item_description.description ; The value of _refine_hist.cycle_id must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_refine_hist.cycle_id' _item.category_id refine_hist _item.mandatory_code yes _item_type.code code save_ save__refine_hist.details _item_description.description ; A description of special aspects of this cycle of the refinement process. ; _item.name '_refine_hist.details' _item.category_id refine_hist _item.mandatory_code no _item_type.code text _item_examples.case ; Residues 13-17 fit and added to model; substantial rebuilding of loop containing residues 43-48; addition of first atoms to solvent model; ten cycles of Prolsq refinement. ; save_ save__refine_hist.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the highest resolution. ; _item.name '_refine_hist.d_res_high' _item.category_id refine_hist _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_hist.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the lowest resolution. ; _item.name '_refine_hist.d_res_low' _item.category_id refine_hist _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_hist.number_atoms_solvent _item_description.description ; The number of solvent atoms that were included in the model at this cycle of the refinement. ; _item.name '_refine_hist.number_atoms_solvent' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_atoms_total _item_description.description ; The total number of atoms that were included in the model at this cycle of the refinement. ; _item.name '_refine_hist.number_atoms_total' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_all _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low. ; _item.name '_refine_hist.number_reflns_all' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion. ; _item.name '_refine_hist.number_reflns_obs' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_hist.number_reflns_R_free' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_R_work _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_hist.number_reflns_R_work' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.R_factor_all _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_all' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_hist.R_factor_obs _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_obs' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_hist.R_factor_R_free _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_R_free' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_hist.R_factor_R_work _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_R_work' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ##################### ## REFINE_LS_RESTR ## ##################### save_refine_ls_restr _category.description ; Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement. ; _category.id refine_ls_restr _category.mandatory_code no _category_key.name '_refine_ls_restr.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal_target _refine_ls_restr.dev_ideal _refine_ls_restr.number _refine_ls_restr.criterion _refine_ls_restr.rejects 'bond_d' 0.020 0.018 1654 '> 2\s' 22 'angle_d' 0.030 0.038 2246 '> 2\s' 139 'planar_d' 0.040 0.043 498 '> 2\s' 21 'planar' 0.020 0.015 270 '> 2\s' 1 'chiral' 0.150 0.177 278 '> 2\s' 2 'singtor_nbd' 0.500 0.216 582 '> 2\s' 0 'multtor_nbd' 0.500 0.207 419 '> 2\s' 0 'xyhbond_nbd' 0.500 0.245 149 '> 2\s' 0 'planar_tor' 3.0 2.6 203 '> 2\s' 9 'staggered_tor' 15.0 17.4 298 '> 2\s' 31 'orthonormal_tor' 20.0 18.1 12 '> 2\s' 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_restr.criterion _item_description.description ; A criterion used to define a parameter value that deviates significantly from its ideal value in the model obtained by restrained least-squares refinement. ; _item.name '_refine_ls_restr.criterion' _item.category_id refine_ls_restr _item.mandatory_code no _item_type.code text _item_examples.case '> 3\s' save_ save__refine_ls_restr.dev_ideal _item_description.description ; For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 \%A (r.m.s.) from ideal values in the current model. ; _item.name '_refine_ls_restr.dev_ideal' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_ls_restr.dev_ideal_target _item_description.description ; For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. ; _item.name '_refine_ls_restr.dev_ideal_target' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_ls_restr.number _item_description.description ; The number of parameters of this type subjected to restraint in least-squares refinement. ; _item.name '_refine_ls_restr.number' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_restr.rejects _item_description.description ; The number of parameters of this type that deviate from ideal values by more than the amount defined in _refine_ls_restr.criterion in the model obtained by restrained least-squares refinement. ; _item.name '_refine_ls_restr.rejects' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_restr.type _item_description.description ; The type of the parameter being restrained. Explicit sets of data values are provided for the programs PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with RESTRAIN_). As computer programs change, these data values are given as examples, not as an enumeration list. Computer programs that convert a data block to a refinement table will expect the exact form of the data values given here to be used. ; loop_ _item.name _item.category_id _item.mandatory_code '_refine_ls_restr.type' refine_ls_restr yes '_refine_ls_restr_type.type' refine_ls_restr_type yes loop_ _item_linked.child_name _item_linked.parent_name '_refine_ls_restr_type.type' '_refine_ls_restr.type' _item_type.code line loop_ _item_examples.case _item_examples.detail 'p_bond_d' 'bond distance' 'p_angle_d' 'bond angle expressed as a distance' 'p_planar_d' 'planar 1,4 distance' 'p_xhbond_d' 'X-H bond distance' 'p_xhangle_d' 'X-H bond angle expressed as a distance' 'p_hydrog_d' 'hydrogen distance' 'p_special_d' 'special distance' 'p_planar' 'planes' 'p_chiral' 'chiral centres' 'p_singtor_nbd' 'single-torsion non-bonded contact' 'p_multtor_nbd' 'multiple-torsion non-bonded contact' 'p_xyhbond_nbd' 'possible (X...Y) hydrogen bond' 'p_xhyhbond_nbd' 'possible (X-H...Y) hydrogen bond' 'p_special_tor' 'special torsion angle' 'p_planar_tor' 'planar torsion angle' 'p_staggered_tor' 'staggered torsion angle' 'p_orthonormal_tor' 'orthonormal torsion angle' 'p_mcbond_it' 'main-chain bond isotropic displacement parameter' 'p_mcangle_it' 'main-chain angle isotropic displacement parameter' 'p_scbond_it' 'side-chain bond isotropic displacement parameter' 'p_scangle_it' 'side-chain angle isotropic displacement parameter' 'p_xhbond_it' 'X-H bond isotropic displacement parameter' 'p_xhangle_it' 'X-H angle isotropic displacement parameter' 'p_special_it' 'special isotropic displacement parameter' 'RESTRAIN_Distances < 2.12' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range less than 2.12 Angstroms. ; 'RESTRAIN_Distances 2.12 < D < 2.625' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range 2.12 - 2.625 Angstroms. ; 'RESTRAIN_Distances > 2.625' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range greater than 2.625 Angstroms. ; 'RESTRAIN_Peptide Planes' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for peptide planes. ; 'RESTRAIN_Ring and other planes' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for rings and planes other than peptide planes. ; 'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4' . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6' . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0' . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2' . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4' . 'RESTRAIN_rms diffs for Uiso atoms at dist >2.4' . save_ save__refine_ls_restr.weight _item_description.description ; The weighting value applied to this type of restraint in the least-squares refinement. ; _item.name '_refine_ls_restr.weight' _item.category_id refine_ls_restr _item.mandatory_code no _item_type.code float save_ ######################### ## REFINE_LS_RESTR_NCS ## ######################### save_refine_ls_restr_ncs _category.description ; Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement. It is expected that these values will only be reported once for each set of restrained domains. ; _category.id refine_ls_restr_ncs _category.mandatory_code no _category_key.name '_refine_ls_restr_ncs.dom_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; _refine_ls_restr_ncs.dom_id d2 _refine_ls_restr_ncs.weight_position 300.0 _refine_ls_restr_ncs.weight_B_iso 2.0 _refine_ls_restr_ncs.rms_dev_position 0.09 _refine_ls_restr_ncs.rms_dev_B_iso 0.16 _refine_ls_restr_ncs.ncs_model_details ; NCS restraint for pseudo-twofold symmetry between domains d1 and d2. Position weight coefficient given in Kcal/(mol \%A^2^) and isotropic B weight coefficient given in \%A^2^. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_restr_ncs.dom_id _item_description.description ; This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_refine_ls_restr_ncs.dom_id' _item.category_id refine_ls_restr_ncs _item.mandatory_code yes _item_type.code code save_ save__refine_ls_restr_ncs.ncs_model_details _item_description.description ; Special aspects of the manner in which noncrystallographic restraints were applied to atomic parameters in the domain specified by _refine_ls_restr_ncs.dom_id and equivalent atomic parameters in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.ncs_model_details' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code text save_ save__refine_ls_restr_ncs.rms_dev_B_iso _item_description.description ; The root-mean-square deviation in equivalent isotropic displacement parameters in the domain specified by _refine_ls_restr_ncs.dom_id and in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.rms_dev_B_iso' _item.category_id refine_ls_restr_ncs _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms_squared save_ save__refine_ls_restr_ncs.rms_dev_position _item_description.description ; The root-mean-square deviation in equivalent atom positions in the domain specified by _refine_ls_restr_ncs.dom_id and in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.rms_dev_position' _item.category_id refine_ls_restr_ncs _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_ncs.weight_B_iso _item_description.description ; The value of the weighting coefficient used in noncrystallographic symmetry restraint of isotropic displacement parameters in the domain specified by _refine_ls_restr_ncs.dom_id to equivalent isotropic displacement parameters in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.weight_B_iso' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code float save_ save__refine_ls_restr_ncs.weight_position _item_description.description ; The value of the weighting coefficient used in noncrystallographic symmetry restraint of atom positions in the domain specified by _refine_ls_restr_ncs.dom_id to equivalent atom positions in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.weight_position' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code float save_ ########################## ## REFINE_LS_RESTR_TYPE ## ########################## save_refine_ls_restr_type _category.description ; Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement. ; _category.id refine_ls_restr_type _category.mandatory_code no _category_key.name '_refine_ls_restr_type.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. ; ; loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target 'RESTRAIN_Distances < 2.12' 509 0.005 0.022 'RESTRAIN_Distances 2.12 < D < 2.625' 671 0.016 0.037 'RESTRAIN_Distances > 2.625' 39 0.034 0.043 'RESTRAIN_Peptide Planes' 59 0.002 0.010 'RESTRAIN_Ring and other planes' 26 0.014 0.010 'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4' 212 0.106 . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6' 288 0.101 . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0' 6 0.077 . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2' 10 0.114 . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4' 215 0.119 . 'RESTRAIN_rms diffs for Uiso atoms at dist >2.4' 461 0.106 . loop_ _refine_ls_restr_type.type _refine_ls_restr_type.distance_cutoff_low _refine_ls_restr_type.distance_cutoff_high 'RESTRAIN_Distances < 2.12' . 2.12 'RESTRAIN_Distances 2.12 < D < 2.625' 2.12 2.625 'RESTRAIN_Distances > 2.625' 2.625 . 'RESTRAIN_Peptide Planes' . . 'RESTRAIN_Ring and other planes' . . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4' 1.2 1.4 'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6' 1.4 1.6 'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0' 1.8 2.0 'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2' 2.0 2.2 'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4' 2.2 2.4 'RESTRAIN_rms diffs for Uiso atoms at dist >2.4' 2.4 . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_restr_type.distance_cutoff_high _item_description.description ; The upper limit in angstroms of the distance range applied to the current restraint type. ; _item.name '_refine_ls_restr_type.distance_cutoff_high' _item.category_id refine_ls_restr_type _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_type.distance_cutoff_low _item_description.description ; The lower limit in angstroms of the distance range applied to the current restraint type. ; _item.name '_refine_ls_restr_type.distance_cutoff_low' _item.category_id refine_ls_restr_type _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_type.type _item_description.description ; This data item is a pointer to _refine_ls_restr.type in the REFINE_LS_RESTR category. ; _item.name '_refine_ls_restr_type.type' _item.category_id refine_ls_restr_type _item.mandatory_code yes _item_type.code line save_ ##################### ## REFINE_LS_SHELL ## ##################### save_refine_ls_shell _category.description ; Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution. ; _category.id refine_ls_shell _category.mandatory_code no loop_ _category_key.name '_refine_ls_shell.d_res_low' '_refine_ls_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_ls_shell.d_res_low _refine_ls_shell.d_res_high _refine_ls_shell.number_reflns_obs _refine_ls_shell.R_factor_obs 8.00 4.51 1226 0.196 4.51 3.48 1679 0.146 3.48 2.94 2014 0.160 2.94 2.59 2147 0.182 2.59 2.34 2127 0.193 2.34 2.15 2061 0.203 2.15 2.00 1647 0.188 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_shell.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. ; _item.name '_refine_ls_shell.d_res_high' _item.category_id refine_ls_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_shell.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. ; _item.name '_refine_ls_shell.d_res_low' _item.category_id refine_ls_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_shell.number_reflns_all _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. ; _item.name '_refine_ls_shell.number_reflns_all' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.number_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. ; _item.name '_refine_ls_shell.number_reflns_obs' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.number_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_ls_shell.number_reflns_R_free' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.number_reflns_R_work _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_ls_shell.number_reflns_R_work' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.percent_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. ; _item.name '_refine_ls_shell.percent_reflns_obs' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.percent_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the reflection limits. ; _item.name '_refine_ls_shell.percent_reflns_R_free' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.R_factor_all _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_all' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.wR_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.R_factor_obs _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_obs' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.wR_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.R_factor_R_free _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_R_free' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.wR_factor_R_free' alternate '_refine_ls_shell.R_factor_R_free_error' associated_error _item_type.code float save_ save__refine_ls_shell.R_factor_R_free_error _item_description.description ; The estimated error in _refine_ls_shell.R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details. ; _item.name '_refine_ls_shell.R_factor_R_free_error' _item.category_id refine_ls_shell _item.mandatory_code no _item_related.related_name '_refine_ls_shell.R_factor_R_free' _item_related.function_code associated_value _item_type.code float save_ save__refine_ls_shell.R_factor_R_work _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_R_work' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.wR_factor_R_work' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.redundancy_reflns_all _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine_ls_shell.redundancy_reflns_all' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.redundancy_reflns_obs _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine_ls_shell.redundancy_reflns_obs' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.wR_factor_all _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_all' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.wR_factor_obs _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_obs' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.wR_factor_R_free _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_R_free' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_R_free' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.wR_factor_R_work _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_R_work' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_R_work' _item_related.function_code alternate _item_type.code float save_ ###################### ## REFINE_OCCUPANCY ## ###################### save_refine_occupancy _category.description ; Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement. ; _category.id refine_occupancy _category.mandatory_code no _category_key.name '_refine_occupancy.class' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.value _refine_occupancy.details 'protein' fix 1.00 . 'solvent' fix 1.00 . 'inhibitor orientation 1' fix 0.65 . 'inhibitor orientation 2' fix 0.35 ; The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_occupancy.class _item_description.description ; The class of atoms treated similarly for occupancy refinement. ; _item.name '_refine_occupancy.class' _item.category_id refine_occupancy _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'all' 'protein' 'solvent' 'sugar-phosphate backbone' save_ save__refine_occupancy.details _item_description.description ; A description of special aspects of the occupancy refinement for a class of atoms described in _refine_occupancy.class. ; _item.name '_refine_occupancy.details' _item.category_id refine_occupancy _item.mandatory_code no _item_type.code text _item_examples.case ; The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. ; save_ save__refine_occupancy.treatment _item_description.description ; The treatment of occupancies for a class of atoms described in _refine_occupancy.class. ; _item.name '_refine_occupancy.treatment' _item.category_id refine_occupancy _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail fix 'fixed' ref 'refined' save_ save__refine_occupancy.value _item_description.description ; The value of occupancy assigned to a class of atoms defined in _refine_occupancy.class. Meaningful only for atoms with fixed occupancy. ; _item.name '_refine_occupancy.value' _item.category_id refine_occupancy _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float loop_ _item_examples.case 1.0 0.41 save_ ########### ## REFLN ## ########### save_refln _category.description ; Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; _category.id refln _category.mandatory_code no loop_ _category_key.name '_refln.index_h' '_refln.index_k' '_refln.index_l' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [Acta Cryst. (1993), C49, 1352-1354]. ; ; loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_squared_calc _refln.F_squared_meas _refln.F_squared_sigma _refln.status 2 0 0 85.57 58.90 1.45 o 3 0 0 15718.18 15631.06 30.40 o 4 0 0 55613.11 49840.09 61.86 o 5 0 0 246.85 241.86 10.02 o 6 0 0 82.16 69.97 1.93 o 7 0 0 1133.62 947.79 11.78 o 8 0 0 2558.04 2453.33 20.44 o 9 0 0 283.88 393.66 7.79 o 10 0 0 283.70 171.98 4.26 o ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refln.A_calc _item_description.description ; The calculated value of structure-factor component A in electrons. A = |F|cos(phase) ; _item.name '_refln.A_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_A_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.A_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.A_calc_au _item_description.description ; The calculated value of structure-factor component A in arbitrary units. A = |F|cos(phase) ; _item.name '_refln.A_calc_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.A_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.A_meas _item_description.description ; The measured value of structure-factor component A in electrons. A = |F|cos(phase) ; _item.name '_refln.A_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_A_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.A_meas_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.A_meas_au _item_description.description ; The measured value of structure-factor component A in arbitrary units. A = |F|cos(phase) ; _item.name '_refln.A_meas_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.A_meas' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.B_calc _item_description.description ; The calculated value of structure-factor component B in electrons. B = |F|sin(phase) ; _item.name '_refln.B_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_B_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.B_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.B_calc_au _item_description.description ; The calculated value of structure-factor component B in arbitrary units. B = |F|sin(phase) ; _item.name '_refln.B_calc_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.B_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.B_meas _item_description.description ; The measured value of structure-factor component B in electrons. B = |F|sin(phase) ; _item.name '_refln.B_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_B_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.B_meas_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.B_meas_au _item_description.description ; The measured value of structure-factor component B in arbitrary units. B = |F|sin(phase) ; _item.name '_refln.B_meas_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.B_meas' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_refln.crystal_id' _item.mandatory_code yes _item_aliases.alias_name '_refln_crystal_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__refln.F_calc _item_description.description ; The calculated value of the structure factor in electrons. ; _item.name '_refln.F_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.F_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.F_calc_au _item_description.description ; The calculated value of the structure factor in arbitrary units. ; _item.name '_refln.F_calc_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.F_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.F_meas _item_description.description ; The measured value of the structure factor in electrons. ; _item.name '_refln.F_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_refln.F_meas_sigma' associated_esd '_refln.F_meas_au' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code electrons save_ save__refln.F_meas_au _item_description.description ; The measured value of the structure factor in arbitrary units. ; _item.name '_refln.F_meas_au' _item.category_id refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_refln.F_meas_sigma_au' associated_esd '_refln.F_meas' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.F_meas_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _refln.F_meas in electrons. ; _item.name '_refln.F_meas_sigma' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_refln.F_meas' associated_value '_refln.F_meas_sigma_au' conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.F_meas_sigma_au _item_description.description ; The standard uncertainty (estimated standard deviation) of _refln.F_meas_au in arbitrary units. ; _item.name '_refln.F_meas_sigma_au' _item.category_id refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_refln.F_meas_au' associated_value '_refln.F_meas_sigma' conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.F_squared_calc _item_description.description ; The calculated value of the squared structure factor in electrons squared. ; _item.name '_refln.F_squared_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code electrons_squared save_ save__refln.F_squared_meas _item_description.description ; The measured value of the squared structure factor in electrons squared. ; _item.name '_refln.F_squared_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code electrons_squared save_ save__refln.F_squared_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared. ; _item.name '_refln.F_squared_sigma' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code electrons_squared save_ save__refln.fom _item_description.description ; The figure of merit m for this reflection. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_refln.fom' _item.category_id refln _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refln.index_h _item_description.description ; Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_h' _item.category_id refln _item.mandatory_code yes _item_aliases.alias_name '_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_refln.index_k' '_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln.index_k _item_description.description ; Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_k' _item.category_id refln _item.mandatory_code yes _item_aliases.alias_name '_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_refln.index_h' '_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln.index_l _item_description.description ; Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_l' _item.category_id refln _item.mandatory_code yes _item_aliases.alias_name '_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_refln.index_h' '_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__refln.intensity_calc _item_description.description ; The calculated value of the intensity in the same units as _refln.intensity_meas. ; _item.name '_refln.intensity_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__refln.intensity_meas _item_description.description ; The measured value of the intensity. ; _item.name '_refln.intensity_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__refln.intensity_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the intensity in the same units as _refln.intensity_meas. ; _item.name '_refln.intensity_sigma' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ #save__refln.mean_path_length_tbar # _item_description.description #; Mean path length in millimetres through the crystal for this # reflection. #; # _item.name '_refln.mean_path_length_tbar' # _item.category_id refln # _item.mandatory_code no # _item_aliases.alias_name '_refln_mean_path_length_tbar' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # _item_type.code float # _item_units.code millimetres # save_ save__refln.status _item_description.description ; Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. ; _item.name '_refln.status' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_observed_status' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value o _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail o ; satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, observed by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable ; < ; satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, unobserved by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine.ls_d_res_high' l 'does not satisfy _refine.ls_d_res_low' f ; satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, observed by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable, excluded from refinement so as to be included in the calculation of a 'free' R factor ; save_ save__refln.phase_calc _item_description.description ; The calculated structure-factor phase in degrees. ; _item.name '_refln.phase_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_phase_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__refln.phase_meas _item_description.description ; The measured structure-factor phase in degrees. ; _item.name '_refln.phase_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_phase_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__refln.refinement_status _item_description.description ; Status of a reflection in the structure-refinement process. ; _item.name '_refln.refinement_status' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_refinement_status' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value incl _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail incl 'included in ls process' excl 'excluded from ls process' extn 'excluded due to extinction' save_ save__refln.scale_group_code _item_description.description ; This data item is a pointer to _reflns_scale.group_code in the REFLNS_SCALE category. ; _item.name '_refln.scale_group_code' _item.mandatory_code yes _item_aliases.alias_name '_refln_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__refln.sint_over_lambda _item_description.description ; The (sin theta)/lambda value in reciprocal angstroms for this reflection. ; _item.name '_refln.sint_over_lambda' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_sint/lambda' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code reciprocal_angstroms save_ save__refln.symmetry_epsilon _item_description.description ; The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. ; _item.name '_refln.symmetry_epsilon' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_symmetry_epsilon' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 48 48 48 1 1 1 _item_type.code int save_ save__refln.symmetry_multiplicity _item_description.description ; The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor magnitudes because of the space-group symmetry and the Friedel relationship. ; _item.name '_refln.symmetry_multiplicity' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_symmetry_multiplicity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 48 48 48 1 1 1 _item_type.code int save_ save__refln.wavelength _item_description.description ; The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. ; _item.name '_refln.wavelength' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refln.wavelength_id _item_description.description ; This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category. ; _item.name '_refln.wavelength_id' _item.mandatory_code yes _item_aliases.alias_name '_refln_wavelength_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ ################### ## REFLN_SYS_ABS ## ################### save_refln_sys_abs _category.description ; Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group. ; _category.id refln_sys_abs _category.mandatory_code no loop_ _category_key.name '_refln_sys_abs.index_h' '_refln_sys_abs.index_k' '_refln_sys_abs.index_l' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _refln_sys_abs.index_h _refln_sys_abs.index_k _refln_sys_abs.index_l _refln_sys_abs.I _refln_sys_abs.sigmaI _refln_sys_abs.I_over_sigmaI 0 3 0 28.32 22.95 1.23 0 5 0 14.11 16.38 0.86 0 7 0 114.81 20.22 5.67 0 9 0 32.99 24.51 1.35 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refln_sys_abs.I _item_description.description ; The measured value of the intensity in arbitrary units. ; _item.name '_refln_sys_abs.I' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.I' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_related.related_name _item_related.function_code '_refln_sys_abs.sigmaI' associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln_sys_abs.I_over_sigmaI _item_description.description ; The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used to evaluate whether a reflection that should be systematically absent according to the designated space group is in fact absent. ; _item.name '_refln_sys_abs.I_over_sigmaI' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.I_over_sigma' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refln_sys_abs.index_h _item_description.description ; Miller index h of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_h' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.h' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_k' '_refln_sys_abs.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.index_k _item_description.description ; Miller index k of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_k' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.k' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_h' '_refln_sys_abs.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.index_l _item_description.description ; Miller index l of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_l' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.l' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_h' '_refln_sys_abs.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.sigmaI _item_description.description ; The standard uncertainty (estimated standard deviation) of _refln_sys_abs.I in arbitrary units. ; _item.name '_refln_sys_abs.sigmaI' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.sigmaI' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_related.related_name _item_related.function_code '_refln_sys_abs.I' associated_value _item_type.code float _item_units.code arbitrary save_ ############ ## REFLNS ## ############ save_reflns _category.description ; Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; _category.id reflns _category.mandatory_code no _category_key.name '_reflns.entry_id' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _reflns.entry_id '5HVP' _reflns.data_reduction_method ; Xengen program scalei. Anomalous pairs were merged. Scaling proceeded in several passes, beginning with 1-parameter fit and ending with 3-parameter fit. ; _reflns.data_reduction_details ; Merging and scaling based on only those reflections with I > \s(I). ; _reflns.d_resolution_high 2.00 _reflns.d_resolution_low 8.00 _reflns.limit_h_max 22 _reflns.limit_h_min 0 _reflns.limit_k_max 46 _reflns.limit_k_min 0 _reflns.limit_l_max 57 _reflns.limit_l_min 0 _reflns.number_obs 7228 _reflns.observed_criterion '> 1 \s(I)' _reflns.details none ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _reflns.limit_h_min 0 _reflns.limit_h_max 6 _reflns.limit_k_min 0 _reflns.limit_k_max 17 _reflns.limit_l_min 0 _reflns.limit_l_max 22 _reflns.number_all 1592 _reflns.number_obs 1408 _reflns.observed_criterion F_>_6.0_\s(F) _reflns.d_resolution_high 0.8733 _reflns.d_resolution_low 11.9202 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns.B_iso_Wilson_estimate _item_description.description ; The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot. ; _item.name '_reflns.B_iso_Wilson_estimate' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__reflns.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_reflns.entry_id' _item.mandatory_code yes save_ save__reflns.data_reduction_details _item_description.description ; A description of special aspects of the data-reduction procedures. ; _item.name '_reflns.data_reduction_details' _item.category_id reflns _item.mandatory_code no _item_type.code text _item_examples.case ; Merging and scaling based on only those reflections with I > sig(I). ; save_ save__reflns.data_reduction_method _item_description.description ; The method used for data reduction. Note that this is not the computer program used, which is described in the SOFTWARE category, but the method itself. This data item should be used to describe significant methodological options used within the data-reduction programs. ; _item.name '_reflns.data_reduction_method' _item.category_id reflns _item.mandatory_code no _item_type.code text _item_examples.case ; Profile fitting by method of Kabsch (1987). Scaling used spherical harmonic coefficients. ; save_ save__reflns.d_resolution_high _item_description.description ; The smallest value for the interplanar spacings for the reflection data. This is called the highest resolution. ; _item.name '_reflns.d_resolution_high' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_d_resolution_high' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns.d_resolution_low _item_description.description ; The largest value for the interplanar spacings for the reflection data. This is called the lowest resolution. ; _item.name '_reflns.d_resolution_low' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_d_resolution_low' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns.details _item_description.description ; A description of reflection data not covered by other data names. This should include details of the Friedel pairs. ; _item.name '_reflns.details' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__reflns.limit_h_max _item_description.description ; Maximum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_max. ; _item.name '_reflns.limit_h_max' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_h_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_h_min _item_description.description ; Minimum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_min. ; _item.name '_reflns.limit_h_min' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_h_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_k_max _item_description.description ; Maximum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_max. ; _item.name '_reflns.limit_k_max' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_k_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_k_min _item_description.description ; Minimum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_min. ; _item.name '_reflns.limit_k_min' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_k_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_l_max _item_description.description ; Maximum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_max. ; _item.name '_reflns.limit_l_max' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_l_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_l_min _item_description.description ; Minimum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_min. ; _item.name '_reflns.limit_l_min' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_l_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.number_all _item_description.description ; The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The item _reflns.details describes the reflection data. ; _item.name '_reflns.number_all' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_number_total' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__reflns.number_obs _item_description.description ; The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see _reflns.observed_criterion). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. ; _item.name '_reflns.number_obs' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_number_observed' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__reflns.observed_criterion _item_description.description ; The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. ; _item.name '_reflns.observed_criterion' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_observed_criterion' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion_sigma_F' alternate '_reflns.observed_criterion_sigma_I' alternate '_reflns.observed_criterion_I_min' alternate '_reflns.observed_criterion_I_max' alternate '_reflns.observed_criterion_F_min' alternate '_reflns.observed_criterion_F_max' alternate _item_type.code text _item_examples.case '>2sigma(I)' save_ save__reflns.observed_criterion_F_max _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of F. ; _item.name '_reflns.observed_criterion_F_max' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_I_max' convention _item_type.code float save_ save__reflns.observed_criterion_F_min _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of F. ; _item.name '_reflns.observed_criterion_F_min' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_I_min' convention _item_type.code float save_ save__reflns.observed_criterion_I_max _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of I. ; _item.name '_reflns.observed_criterion_I_max' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_F_max' convention _item_type.code float save_ save__reflns.observed_criterion_I_min _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of I. ; _item.name '_reflns.observed_criterion_I_min' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_F_min' convention _item_type.code float save_ save__reflns.observed_criterion_sigma_F _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(F). ; _item.name '_reflns.observed_criterion_sigma_F' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_sigma_I' convention _item_type.code float save_ save__reflns.observed_criterion_sigma_I _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(I). ; _item.name '_reflns.observed_criterion_sigma_I' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_sigma_F' convention _item_type.code float save_ save__reflns.percent_possible_obs _item_description.description ; The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. ; _item.name '_reflns.percent_possible_obs' _item.category_id reflns _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns.R_free_details _item_description.description ; A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a 'free' R factor. ; _item.name '_reflns.R_free_details' _item.category_id reflns _item.mandatory_code no _item_type.code text _item_examples.case ; The data set was sorted with l varying most rapidly and h varying least rapidly. Every 10th reflection in this sorted list was excluded from refinement and included in the calculation of a 'free' R factor. ; save_ save__reflns.Rmerge_F_all _item_description.description ; Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns.Rmerge_F_all' _item.category_id reflns _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns.Rmerge_F_obs _item_description.description ; Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns.Rmerge_F_obs' _item.category_id reflns _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################## ## REFLNS_SCALE ## ################## save_reflns_scale _category.description ; Data items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through _refln.scale_group_code. ; _category.id reflns_scale _category.mandatory_code no _category_key.name '_reflns_scale.group_code' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. ; ; _reflns_scale.group_code SG1 _reflns_scale.meas_F 4.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns_scale.group_code _item_description.description ; The code identifying a scale _reflns_scale.meas_F, _reflns_scale.meas_F_squared or _reflns_scale.meas_intensity. These are linked to the REFLN list by the _refln.scale_group_code. These codes need not correspond to those in the DIFFRN_SCALE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_reflns_scale.group_code' reflns_scale yes '_refln.scale_group_code' refln yes _item_aliases.alias_name '_reflns_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_refln.scale_group_code' '_reflns_scale.group_code' _item_type.code line loop_ _item_examples.case '1' '2' 'c1' 'c2' save_ save__reflns_scale.meas_F _item_description.description ; A scale associated with _reflns_scale.group_code. ; _item.name '_reflns_scale.meas_F' _item.category_id reflns_scale _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_F' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_scale.meas_F_squared _item_description.description ; A scale associated with _reflns_scale.group_code. ; _item.name '_reflns_scale.meas_F_squared' _item.category_id reflns_scale _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_F_squared' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_scale.meas_intensity _item_description.description ; A scale associated with _reflns_scale.group_code. ; _item.name '_reflns_scale.meas_intensity' _item.category_id reflns_scale _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_intensity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################## ## REFLNS_SHELL ## ################## save_reflns_shell _category.description ; Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution. ; _category.id reflns_shell _category.mandatory_code no loop_ _category_key.name '_reflns_shell.d_res_high' '_reflns_shell.d_res_low' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_obs 31.38 3.82 69.8 9024 2540 96.8 1.98 3.82 3.03 26.1 7413 2364 95.1 3.85 3.03 2.65 10.5 5640 2123 86.2 6.37 2.65 2.41 6.4 4322 1882 76.8 8.01 2.41 2.23 4.3 3247 1714 70.4 9.86 2.23 2.10 3.1 1140 812 33.3 13.99 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns_shell.d_res_high _item_description.description ; The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. ; _item.name '_reflns_shell.d_res_high' _item.category_id reflns_shell _item.mandatory_code yes _item_aliases.alias_name '_reflns_shell_d_res_high' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns_shell.d_res_low _item_description.description ; The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. ; _item.name '_reflns_shell.d_res_low' _item.category_id reflns_shell _item.mandatory_code yes _item_aliases.alias_name '_reflns_shell_d_res_low' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns_shell.meanI_over_sigI_all _item_description.description ; The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. ; _item.name '_reflns_shell.meanI_over_sigI_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_meanI_over_sigI_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__reflns_shell.meanI_over_sigI_obs _item_description.description ; The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns.observed_criterion) in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell. ; _item.name '_reflns_shell.meanI_over_sigI_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_meanI_over_sigI_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__reflns_shell.number_measured_all _item_description.description ; The total number of reflections measured for this shell. ; _item.name '_reflns_shell.number_measured_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_measured_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.number_measured_obs _item_description.description ; The number of reflections classified as 'observed' (see _reflns.observed_criterion) for this shell. ; _item.name '_reflns_shell.number_measured_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_measured_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.number_possible _item_description.description ; The number of unique reflections it is possible to measure in this shell. ; _item.name '_reflns_shell.number_possible' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_possible' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__reflns_shell.number_unique_all _item_description.description ; The total number of measured reflections which are symmetry- unique after merging for this shell. ; _item.name '_reflns_shell.number_unique_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_unique_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.number_unique_obs _item_description.description ; The total number of measured reflections classified as 'observed' (see _reflns.observed_criterion) which are symmetry-unique after merging for this shell. ; _item.name '_reflns_shell.number_unique_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_unique_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.percent_possible_all _item_description.description ; The percentage of geometrically possible reflections represented by all reflections measured for this shell. ; _item.name '_reflns_shell.percent_possible_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_percent_possible_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.percent_possible_obs _item_description.description ; The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see _reflns.observed_criterion) for this shell. ; _item.name '_reflns_shell.percent_possible_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_percent_possible_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_F_all _item_description.description ; Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_F_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_F_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_F_obs _item_description.description ; Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_F_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_F_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_I_all _item_description.description ; The value of Rmerge(I) for all reflections in a given shell. sum~i~(sum~j~|I~j~ - |) Rmerge(I) = -------------------------- sum~i~(sum~j~) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_I_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_I_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_I_obs _item_description.description ; The value of Rmerge(I) for reflections classified as 'observed' (see _reflns.observed_criterion) in a given shell. sum~i~(sum~j~|I~j~ - |) Rmerge(I) = -------------------------- sum~i~(sum~j~) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_I_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_I_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ############## ## SOFTWARE ## ############## save_software _category.description ; Data items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation. These data items allow computer programs to be referenced in more detail than data items in the COMPUTING category do. ; _category.id software _category.mandatory_code no loop_ _category_key.name '_software.name' '_software.version' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.location _software.classification _software.citation_id _software.language _software.compiler_name _software.compiler_version _software.hardware _software.os _software.os_version _software.dependencies _software.mods _software.description Prolsq unknown . program 'Wayne A. Hendrickson' ? 'ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/' refinement ref5 Fortran 'Convex Fortran' v8.0 'Convex C220' ConvexOS v10.1 'Requires that Protin be run first' optimized 'restrained least-squares refinement' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__software.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_software.citation_id' _item.mandatory_code no save_ save__software.classification _item_description.description ; The classification of the program according to its major function. ; _item.name '_software.classification' _item.category_id software _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'data collection' 'data reduction' 'phasing' 'model building' 'refinement' 'validation' 'other' save_ save__software.compiler_name _item_description.description ; The compiler used to compile the software. ; _item.name '_software.compiler_name' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Convex Fortran' 'gcc' 'DEC C' save_ save__software.compiler_version _item_description.description ; The version of the compiler used to compile the software. ; _item.name '_software.compiler_version' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case '3.1' '2.1 alpha' save_ save__software.contact_author _item_description.description ; The recognized contact author of the software. This could be the original author, someone who has modified the code or someone who maintains the code. It should be the person most commonly associated with the code. ; _item.name '_software.contact_author' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'T. Alwyn Jones' 'Axel Brunger' save_ save__software.contact_author_email _item_description.description ; The e-mail address of the person specified in _software.contact_author. ; _item.name '_software.contact_author_email' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'bourne@sdsc.edu' save_ save__software.date _item_description.description ; The date the software was released. ; _item.name '_software.date' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 1991-10-01 1990-04-30 save_ save__software.description _item_description.description ; Description of the software. ; _item.name '_software.description' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'Uses method of restrained least squares' save_ save__software.dependencies _item_description.description ; Any prerequisite software required to run _software.name. ; _item.name '_software.dependencies' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'PDBlib class library' save_ save__software.hardware _item_description.description ; The hardware upon which the software was run. ; _item.name '_software.hardware' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Sun Sparc 10 model 41' 'Dec Alpha 3000 model 500S' 'Silicon Graphics Elan' 'Compaq PC 486/66' save_ save__software.language _item_description.description ; The major computing language in which the software is coded. ; _item.name '_software.language' _item.category_id software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value Ada assembler Awk Basic 'C++' 'C/C++' C csh Fortran Fortran_77 'Fortran 77' 'Fortran 90' Java ksh Pascal Perl Python sh Tcl Other save_ save__software.location _item_description.description ; The URL for an Internet address at which details of the software can be found. ; _item.name '_software.location' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'http://rosebud.sdsc.edu/projects/pb/IUCr/software.html' 'ftp://ftp.sdsc.edu/pub/sdsc/biology/' save_ save__software.mods _item_description.description ; Any noteworthy modifications to the base software, if applicable. ; _item.name '_software.mods' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'Added support for space group F432' save_ save__software.name _item_description.description ; The name of the software. ; _item.name '_software.name' _item.category_id software _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'Merlot' 'O' 'Xengen' 'X-plor' save_ save__software.os _item_description.description ; The name of the operating system under which the software runs. ; _item.name '_software.os' _item.category_id software _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Ultrix' 'OpenVMS' 'DOS' 'Windows 95' 'Windows NT' 'Irix' 'HPUX' 'DEC Unix' save_ save__software.os_version _item_description.description ; The version of the operating system under which the software runs. ; _item.name '_software.os_version' _item.category_id software _item.mandatory_code no _item_type.code text loop_ _item_examples.case '3.1' '4.2.1' save_ save__software.type _item_description.description ; The classification of the software according to the most common types. ; _item.name '_software.type' _item.category_id software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value _item_enumeration.detail program ; individual program with limited functionality ; library ; used by a program at load time ; package ; collections of programs with multiple functionality ; filter ; filters input and output streams ; jiffy ; short, simple program ; other ; all other kinds of software ; save_ save__software.version _item_description.description ; The version of the software. ; _item.name '_software.version' _item.category_id software _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'v1.0' 'beta' '3.1-2' 'unknown' save_ ############ ## STRUCT ## ############ save_struct _category.description ; Data items in the STRUCT category record details about the description of the crystallographic structure. ; _category.id struct _category.mandatory_code no _category_key.name '_struct.entry_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _struct.entry_id '5HVP' _struct.title ; HIV-1 protease complex with acetyl-pepstatin ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_struct.entry_id' _item.mandatory_code yes save_ save__struct.title _item_description.description ; A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. ; _item.name '_struct.title' _item.category_id struct _item.mandatory_code no _item_type.code text loop_ _item_examples.case '5'-D(*(I)CP*CP*GP*G)-3' 'T4 lysozyme mutant - S32A' 'hen egg white lysozyme at -30 degrees C' 'quail egg white lysozyme at 2 atmospheres' save_ ################# ## STRUCT_ASYM ## ################# save_struct_asym _category.description ; Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit. ; _category.id struct_asym _category.mandatory_code no _category_key.name '_struct_asym.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_asym.id _struct_asym.entity_id _struct_asym.details A 1 'one monomer of the dimeric enzyme' B 1 'one monomer of the dimeric enzyme' C 2 'one partially occupied position for the inhibitor' D 2 'one partially occupied position for the inhibitor' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_asym.details _item_description.description ; A description of special aspects of this portion of the contents of the asymmetric unit. ; _item.name '_struct_asym.details' _item.category_id struct_asym _item.mandatory_code no _item_type.code text _item_examples.case ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. ; save_ save__struct_asym.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_struct_asym.entity_id' _item.mandatory_code yes save_ save__struct_asym.id _item_description.description ; The value of _struct_asym.id must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_asym.id' struct_asym yes '_atom_site.label_asym_id' atom_site no '_geom_angle.atom_site_label_asym_id_1' geom_angle no '_geom_angle.atom_site_label_asym_id_2' geom_angle no '_geom_angle.atom_site_label_asym_id_3' geom_angle no '_geom_bond.atom_site_label_asym_id_1' geom_bond no '_geom_bond.atom_site_label_asym_id_2' geom_bond no '_geom_contact.atom_site_label_asym_id_1' geom_contact no '_geom_contact.atom_site_label_asym_id_2' geom_contact no '_geom_hbond.atom_site_label_asym_id_A' geom_hbond no '_geom_hbond.atom_site_label_asym_id_D' geom_hbond no '_geom_hbond.atom_site_label_asym_id_H' geom_hbond no '_geom_torsion.atom_site_label_asym_id_1' geom_torsion no '_geom_torsion.atom_site_label_asym_id_2' geom_torsion no '_geom_torsion.atom_site_label_asym_id_3' geom_torsion no '_geom_torsion.atom_site_label_asym_id_4' geom_torsion no '_struct_biol_gen.asym_id' struct_biol_gen yes '_struct_conf.beg_label_asym_id' struct_conf yes '_struct_conf.end_label_asym_id' struct_conf yes '_struct_conn.ptnr1_label_asym_id' struct_conn yes '_struct_conn.ptnr2_label_asym_id' struct_conn yes '_struct_mon_nucl.label_asym_id' struct_mon_nucl yes '_struct_mon_prot.label_asym_id' struct_mon_prot yes '_struct_mon_prot_cis.label_asym_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_asym_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_asym_id' struct_ncs_dom_lim yes '_struct_sheet_range.beg_label_asym_id' struct_sheet_range yes '_struct_sheet_range.end_label_asym_id' struct_sheet_range yes '_struct_site_gen.label_asym_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_asym_id' '_struct_asym.id' '_struct_biol_gen.asym_id' '_struct_asym.id' '_geom_angle.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_angle.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_angle.atom_site_label_asym_id_3' '_atom_site.label_asym_id' '_geom_bond.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_bond.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_contact.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_contact.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_hbond.atom_site_label_asym_id_A' '_atom_site.label_asym_id' '_geom_hbond.atom_site_label_asym_id_D' '_atom_site.label_asym_id' '_geom_hbond.atom_site_label_asym_id_H' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_3' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_4' '_atom_site.label_asym_id' '_struct_conf.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_conf.end_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr1_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr2_label_asym_id' '_atom_site.label_asym_id' '_struct_mon_nucl.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot_cis.label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_lim.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_lim.end_label_asym_id' '_atom_site.label_asym_id' '_struct_sheet_range.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_sheet_range.end_label_asym_id' '_atom_site.label_asym_id' '_struct_site_gen.label_asym_id' '_atom_site.label_asym_id' _item_type.code code loop_ _item_examples.case '1' 'A' '2B3' save_ ################# ## STRUCT_BIOL ## ################# save_struct_biol _category.description ; Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light- and heavy-chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit. ; _category.id struct_biol _category.mandatory_code no _category_key.name '_struct_biol.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_biol.id _struct_biol.details 1 ; significant deviations from twofold symmetry exist in this dimeric enzyme ; 2 ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (2) is roughly twofold symmetric to biological unit (3). Disorder in the protein chain indicated with alternative ID 1 should be used with this biological unit. ; 3 ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol.details _item_description.description ; A description of special aspects of the biological unit. ; _item.name '_struct_biol.details' _item.category_id struct_biol _item.mandatory_code no _item_type.code text _item_examples.case ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. ; save_ save__struct_biol.id _item_description.description ; The value of _struct_biol.id must uniquely identify a record in the STRUCT_BIOL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_biol.id' struct_biol yes '_struct_biol_gen.biol_id' struct_biol_gen yes '_struct_biol_keywords.biol_id' struct_biol_keywords yes '_struct_biol_view.biol_id' struct_biol_view yes '_struct_ref.biol_id' struct_ref no loop_ _item_linked.child_name _item_linked.parent_name '_struct_biol_gen.biol_id' '_struct_biol.id' '_struct_biol_keywords.biol_id' '_struct_biol.id' '_struct_biol_view.biol_id' '_struct_biol.id' '_struct_ref.biol_id' '_struct_biol.id' _item_type.code line save_ ##################### ## STRUCT_BIOL_GEN ## ##################### save_struct_biol_gen _category.description ; Data items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit. The STRUCT_BIOL_GEN data items provide the specifications of the components that constitute that biological unit, which may include symmetry elements. ; _category.id struct_biol_gen _category.mandatory_code no loop_ _category_key.name '_struct_biol_gen.biol_id' '_struct_biol_gen.asym_id' '_struct_biol_gen.symmetry' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry 1 A 1_555 1 B 1_555 2 A 1_555 2 B 1_555 2 C 1_555 3 A 1_555 3 B 1_555 3 D 1_555 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol_gen.asym_id _item_description.description ; This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_struct_biol_gen.asym_id' _item.mandatory_code yes save_ save__struct_biol_gen.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_biol_gen.biol_id' _item.mandatory_code yes save_ save__struct_biol_gen.details _item_description.description ; A description of special aspects of the symmetry generation of this portion of the biological structure. ; _item.name '_struct_biol_gen.details' _item.category_id struct_biol_gen _item.mandatory_code no _item_type.code text _item_examples.case ; The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. ; save_ save__struct_biol_gen.symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_biol_gen.asym_id to generate a portion of the biological structure. ; _item.name '_struct_biol_gen.symmetry' _item.category_id struct_biol_gen _item.mandatory_code yes # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ########################## ## STRUCT_BIOL_KEYWORDS ## ########################## save_struct_biol_keywords _category.description ; Data items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit. ; _category.id struct_biol_keywords _category.mandatory_code no loop_ _category_key.name '_struct_biol_keywords.biol_id' '_struct_biol_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_biol_keywords.biol_id _struct_biol_keywords.text 1 'aspartyl-protease' 1 'aspartic-protease' 1 'acid-protease' 1 'aspartyl-proteinase' 1 'aspartic-proteinase' 1 'acid-proteinase' 1 'enzyme' 1 'protease' 1 'proteinase' 1 'dimer' 2 'drug-enzyme complex' 2 'inhibitor-enzyme complex' 2 'drug-protease complex' 2 'inhibitor-protease complex' 3 'drug-enzyme complex' 3 'inhibitor-enzyme complex' 3 'drug-protease complex' 3 'inhibitor-protease complex' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol_keywords.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_biol_keywords.biol_id' _item.mandatory_code yes save_ save__struct_biol_keywords.text _item_description.description ; Keywords describing this biological entity. ; _item.name '_struct_biol_keywords.text' _item.category_id struct_biol_keywords _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'antibody' 'antigen' 'enzyme' 'cytokine' 'tRNA' save_ ###################### ## STRUCT_BIOL_VIEW ## ###################### save_struct_biol_view _category.description ; Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure. ; _category.id struct_biol_view _category.mandatory_code no loop_ _category_key.name '_struct_biol_view.biol_id' '_struct_biol_view.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry, (1989), 28, 310-320]. ; ; _struct_biol_view.biol_id c1 _struct_biol_view.id 1 _struct_biol_view.rot_matrix[1][1] 0.132 _struct_biol_view.rot_matrix[1][2] 0.922 _struct_biol_view.rot_matrix[1][3] -0.363 _struct_biol_view.rot_matrix[2][1] 0.131 _struct_biol_view.rot_matrix[2][2] -0.380 _struct_biol_view.rot_matrix[2][3] -0.916 _struct_biol_view.rot_matrix[3][1] -0.982 _struct_biol_view.rot_matrix[3][2] 0.073 _struct_biol_view.rot_matrix[3][3] -0.172 _struct_biol_view.details ; This view highlights the ATAT-Netropsin interaction in the DNA-drug complex. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol_view.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_biol_view.biol_id' _item.mandatory_code yes save_ save__struct_biol_view.details _item_description.description ; A description of special aspects of this view of the biological structure. This data item can be used as a figure legend. ; _item.name '_struct_biol_view.details' _item.category_id struct_biol_view _item.mandatory_code no _item_type.code text _item_examples.case ; The enzyme has been oriented with the molecular twofold axis aligned with the horizontal axis of the figure. ; save_ save__struct_biol_view.id _item_description.description ; The value of _struct_biol_view.id must uniquely identify a record in the STRUCT_BIOL_VIEW list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_biol_view.id' _item.category_id struct_biol_view _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Figure 1' 'unliganded enzyme' 'view down enzyme active site' save_ save__struct_biol_view.rot_matrix[1][1] _item_description.description ; The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[1][1]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[1][2] _item_description.description ; The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[1][2]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[1][3] _item_description.description ; The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[1][3]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[2][1] _item_description.description ; The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[2][1]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[2][2] _item_description.description ; The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[2][2]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[2][3] _item_description.description ; The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[2][3]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[3][1] _item_description.description ; The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[3][1]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[3][2] _item_description.description ; The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[3][2]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[3][3] _item_description.description ; The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[3][3]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ ################# ## STRUCT_CONF ## ################# save_struct_conf _category.description ; Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations. ; _category.id struct_conf _category.mandatory_code no _category_key.name '_struct_conf.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conf.id _struct_conf.conf_type_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.details HELX1 HELX_RH_AL_P ARG A 87 GLN A 92 . HELX2 HELX_RH_AL_P ARG B 287 GLN B 292 . STRN1 STRN_P PRO A 1 LEU A 5 . STRN2 STRN_P CYS B 295 PHE B 299 . STRN3 STRN_P CYS A 95 PHE A 299 . STRN4 STRN_P PRO B 201 LEU B 205 . # - - - - data truncated for brevity - - - - TURN1 TURN_TY1P_P ILE A 15 GLN A 18 . TURN2 TURN_TY2_P GLY A 49 GLY A 52 . TURN3 TURN_TY1P_P ILE A 55 HIS A 69 . TURN4 TURN_TY1_P THR A 91 GLY A 94 . # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conf.beg_label_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_asym_id' _item.mandatory_code yes save_ save__struct_conf.beg_label_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_comp_id' _item.mandatory_code yes save_ save__struct_conf.beg_label_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_seq_id' _item.mandatory_code yes save_ save__struct_conf.beg_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_asym_id' _item.mandatory_code no save_ save__struct_conf.beg_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_comp_id' _item.mandatory_code no save_ save__struct_conf.beg_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_seq_id' _item.mandatory_code no save_ save__struct_conf.conf_type_id _item_description.description ; This data item is a pointer to _struct_conf_type.id in the STRUCT_CONF_TYPE category. ; _item.name '_struct_conf.conf_type_id' _item.mandatory_code yes save_ save__struct_conf.details _item_description.description ; A description of special aspects of the conformation assignment. ; _item.name '_struct_conf.details' _item.category_id struct_conf _item.mandatory_code no _item_type.code text save_ save__struct_conf.end_label_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_asym_id' _item.mandatory_code yes save_ save__struct_conf.end_label_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_comp_id' _item.mandatory_code yes save_ save__struct_conf.end_label_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_seq_id' _item.mandatory_code yes save_ save__struct_conf.end_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_asym_id' _item.mandatory_code no save_ save__struct_conf.end_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_comp_id' _item.mandatory_code no save_ save__struct_conf.end_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_seq_id' _item.mandatory_code no save_ save__struct_conf.id _item_description.description ; The value of _struct_conf.id must uniquely identify a record in the STRUCT_CONF list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_conf.id' _item.category_id struct_conf _item.mandatory_code yes _item_type.code code save_ ###################### ## STRUCT_CONF_TYPE ## ###################### save_struct_conf_type _category.description ; Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer. ; _category.id struct_conf_type _category.mandatory_code no _category_key.name '_struct_conf_type.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conf_type.id _struct_conf_type.criteria _struct_conf_type.reference HELX_RH_AL_P 'author judgement' . STRN_P 'author judgement' . TURN_TY1_P 'author judgement' . TURN_TY1P_P 'author judgement' . TURN_TY2_P 'author judgement' . TURN_TY2P_P 'author judgement' . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conf_type.criteria _item_description.description ; The criteria used to assign this conformation type. ; _item.name '_struct_conf_type.criteria' _item.category_id struct_conf_type _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'author judgement' 'phi=54-74, psi=30-50' save_ save__struct_conf_type.id _item_description.description ; The descriptor that categorizes the type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsion angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conf_type.id' struct_conf_type yes '_struct_conf.conf_type_id' struct_conf yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.conf_type_id' '_struct_conf_type.id' _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail HELX_P ; helix with handedness and type not specified (protein) ; HELX_OT_P ; helix with handedness and type that do not conform to an accepted category (protein) ; # HELX_RH_P ; right-handed helix with type not specified (protein) ; HELX_RH_OT_P ; right-handed helix with type that does not conform to an accepted category (protein) ; HELX_RH_AL_P 'right-handed alpha helix (protein)' HELX_RH_GA_P 'right-handed gamma helix (protein)' HELX_RH_OM_P 'right-handed omega helix (protein)' HELX_RH_PI_P 'right-handed pi helix (protein)' HELX_RH_27_P 'right-handed 2-7 helix (protein)' HELX_RH_3T_P 'right-handed 3-10 helix (protein)' HELX_RH_PP_P 'right-handed polyproline helix (protein)' # HELX_LH_P ; left-handed helix with type not specified (protein) ; HELX_LH_OT_P ; left-handed helix with type that does not conform to an accepted category (protein) ; HELX_LH_AL_P 'left-handed alpha helix (protein)' HELX_LH_GA_P 'left-handed gamma helix (protein)' HELX_LH_OM_P 'left-handed omega helix (protein)' HELX_LH_PI_P 'left-handed pi helix (protein)' HELX_LH_27_P 'left-handed 2-7 helix (protein)' HELX_LH_3T_P 'left-handed 3-10 helix (protein)' HELX_LH_PP_P 'left-handed polyproline helix (protein)' # HELX_N ; helix with handedness and type not specified (nucleic acid) ; HELX_OT_N ; helix with handedness and type that do not conform to an accepted category (nucleic acid) ; # HELX_RH_N ; right-handed helix with type not specified (nucleic acid) ; HELX_RH_OT_N ; right-handed helix with type that does not conform to an accepted category (nucleic acid) ; HELX_RH_A_N 'right-handed A helix (nucleic acid)' HELX_RH_B_N 'right-handed B helix (nucleic acid)' HELX_RH_Z_N 'right-handed Z helix (nucleic acid)' # HELX_LH_N ; left-handed helix with type not specified (nucleic acid) ; HELX_LH_OT_N ; left-handed helix with type that does not conform to an accepted category (nucleic acid) ; HELX_LH_A_N 'left-handed A helix (nucleic acid)' HELX_LH_B_N 'left-handed B helix (nucleic acid)' HELX_LH_Z_N 'left-handed Z helix (nucleic acid)' # TURN_P 'turn with type not specified (protein)' TURN_OT_P ; turn with type that does not conform to an accepted category (protein) ; TURN_TY1_P 'type I turn (protein)' TURN_TY1P_P 'type I prime turn (protein)' TURN_TY2_P 'type II turn (protein)' TURN_TY2P_P 'type II prime turn (protein)' TURN_TY3_P 'type III turn (protein)' TURN_TY3P_P 'type III prime turn (protein)' # STRN 'beta strand (protein)' save_ save__struct_conf_type.reference _item_description.description ; A literature reference that defines the criteria used to assign this conformation type and subtype. ; _item.name '_struct_conf_type.reference' _item.category_id struct_conf_type _item.mandatory_code no _item_type.code text save_ ################# ## STRUCT_CONN ## ################# save_struct_conn _category.description ; Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these connections. ; _category.id struct_conn _category.mandatory_code no _category_key.name '_struct_conn.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_role _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_role _struct_conn.ptnr2_symmetry _struct_conn.details C1 saltbr ARG A 87 NZ1 positive 1_555 GLU A 92 OE1 negative 1_555 . C2 hydrog ARG B 287 N donor 1_555 GLY B 292 O acceptor 1_555 . # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conn.conn_type_id _item_description.description ; This data item is a pointer to _struct_conn_type.id in the STRUCT_CONN_TYPE category. ; _item.name '_struct_conn.conn_type_id' _item.mandatory_code yes save_ save__struct_conn.details _item_description.description ; A description of special aspects of the connection. ; _item.name '_struct_conn.details' _item.category_id struct_conn _item.mandatory_code no _item_type.code text _item_examples.case 'disulfide bridge C-S-S-C is highly distorted' save_ save__struct_conn.id _item_description.description ; The value of _struct_conn.id must uniquely identify a record in the STRUCT_CONN list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_conn.id' _item.category_id struct_conn _item.mandatory_code yes _item_type.code code save_ save__struct_conn.ptnr1_label_alt_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_conn.ptnr1_label_alt_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_label_asym_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_label_asym_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_label_atom_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_struct_conn.ptnr1_label_atom_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_label_comp_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_label_comp_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_label_seq_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_label_seq_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_auth_asym_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_asym_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_auth_atom_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_atom_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_auth_comp_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_comp_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_auth_seq_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_seq_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_role _item_description.description ; The chemical or structural role of the first partner in the structure connection. ; _item.name '_struct_conn.ptnr1_role' _item.category_id struct_conn _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'donor' 'acceptor' 'negative' 'positive' 'metal' 'metal coordination' save_ save__struct_conn.ptnr1_symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr1_label* to generate the first partner in the structure connection. ; _item.name '_struct_conn.ptnr1_symmetry' _item.category_id struct_conn _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__struct_conn.ptnr2_label_alt_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_conn.ptnr2_label_alt_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_label_asym_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_label_asym_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_label_atom_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_struct_conn.ptnr2_label_atom_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_label_comp_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_label_comp_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_label_seq_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_label_seq_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_auth_asym_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_asym_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_auth_atom_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_atom_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_auth_comp_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_comp_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_auth_seq_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_seq_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_role _item_description.description ; The chemical or structural role of the second partner in the structure connection. ; _item.name '_struct_conn.ptnr2_role' _item.category_id struct_conn _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'donor' 'acceptor' 'negative' 'positive' 'metal' 'metal coordination' save_ save__struct_conn.ptnr2_symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr2_label* to generate the second partner in the structure connection. ; _item.name '_struct_conn.ptnr2_symmetry' _item.category_id struct_conn _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ###################### ## STRUCT_CONN_TYPE ## ###################### save_struct_conn_type _category.description ; Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure. ; _category.id struct_conn_type _category.mandatory_code no _category_key.name '_struct_conn_type.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference saltbr 'negative to positive distance > 2.5 \%A, < 3.2 \%A' . hydrog 'NO distance > 2.5\%A, < 3.5\%A, NOC angle < 120 degrees' . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conn_type.criteria _item_description.description ; The criteria used to define the interaction. ; _item.name '_struct_conn_type.criteria' _item.category_id struct_conn_type _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'O to N distance > 2.5 \%A, < 3.2 \%A' 'authors judgement' save_ save__struct_conn_type.id _item_description.description ; The chemical or structural type of the interaction. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conn_type.id' struct_conn_type yes '_struct_conn.conn_type_id' struct_conn yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conn.conn_type_id' '_struct_conn_type.id' _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail covale 'covalent bond' disulf 'disulfide bridge' hydrog 'hydrogen bond' metalc 'metal coordination' mismat 'mismatched base pairs' saltbr 'ionic interaction' modres 'covalent residue modification' covale_base 'covalent modification of a nucleotide base' covale_sugar 'covalent modification of a nucleotide sugar' covale_phosphate 'covalent modification of a nucleotide phosphate' save_ save__struct_conn_type.reference _item_description.description ; A reference that specifies the criteria used to define the interaction. ; _item.name '_struct_conn_type.reference' _item.category_id struct_conn_type _item.mandatory_code no _item_type.code text save_ ##################### ## STRUCT_KEYWORDS ## ##################### save_struct_keywords _category.description ; Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry. ; _category.id struct_keywords _category.mandatory_code no _category_key.name '_struct_keywords.entry_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_keywords.entry_id _struct_keywords.text '5HVP' 'enzyme-inhibitor complex, aspartyl protease, static disorder' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_keywords.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_struct_keywords.entry_id' _item.mandatory_code yes save_ save__struct_keywords.text _item_description.description ; Keywords describing this structure. ; _item.name '_struct_keywords.text' _item.category_id struct_keywords _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'serine protease' 'inhibited complex' 'high-resolution refinement' save_ ######################## ## STRUCT_MON_DETAILS ## ######################## save_struct_mon_details _category.description ; Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on. ; _category.id struct_mon_details _category.mandatory_code no _category_key.name '_struct_mon_details.entry_id' loop_ _category_group.id 'inclusive_group' 'struct_group' save_ save__struct_mon_details.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_struct_mon_details.entry_id' _item.mandatory_code yes save_ save__struct_mon_details.prot_cis _item_description.description ; An ideal cis peptide bond would have an omega torsion angle of zero. This data item gives the value in degrees by which the observed torsion angle can differ from 0.0 and still be considered cis. ; _item.name '_struct_mon_details.prot_cis' _item.category_id struct_mon_details _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 30.0 save_ save__struct_mon_details.RSCC _item_description.description ; This data item describes the specifics of the calculations that generated the values given in _struct_mon_prot.RSCC_all, _struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. ; _item.name '_struct_mon_details.RSCC' _item.category_id struct_mon_details _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. ; ; The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. ; save_ save__struct_mon_details.RSR _item_description.description ; This data item describes the specifics of the calculations that generated the values given in _struct_mon_prot.RSR_all, _struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. ; _item.name '_struct_mon_details.RSR' _item.category_id struct_mon_details _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. ; ; The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. ; save_ ##################### ## STRUCT_MON_NUCL ## ##################### save_struct_mon_nucl _category.description ; Data items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level. Analogous data items for proteins are given in the STRUCT_MON_PROT category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. ; _category.id struct_mon_nucl _category.mandatory_code no loop_ _category_key.name '_struct_mon_nucl.label_alt_id' '_struct_mon_nucl.label_asym_id' '_struct_mon_nucl.label_comp_id' '_struct_mon_nucl.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure BDL028. ; ; loop_ _struct_mon_nucl.label_comp_id _struct_mon_nucl.label_seq_id _struct_mon_nucl.label_asym_id _struct_mon_nucl.label_alt_id _struct_mon_nucl.alpha _struct_mon_nucl.beta _struct_mon_nucl.gamma _struct_mon_nucl.delta _struct_mon_nucl.epsilon _struct_mon_nucl.zeta C 1 A . . . 29.9 131.9 222.1 174.2 G 2 A . 334.0 130.6 33.1 125.6 167.6 270.9 T 3 A . 258.2 178.7 101.0 114.6 216.6 259.3 # ---- abbreviated list ----- ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_mon_nucl.alpha _item_description.description ; The value in degrees of the backbone torsion angle alpha (O3'-P-O5'-C5'). ; _item.name '_struct_mon_nucl.alpha' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.auth_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.auth_asym_id' _item.mandatory_code no save_ save__struct_mon_nucl.auth_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.auth_comp_id' _item.mandatory_code no save_ save__struct_mon_nucl.auth_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.auth_seq_id' _item.mandatory_code no save_ save__struct_mon_nucl.beta _item_description.description ; The value in degrees of the backbone torsion angle beta (P-O5'-C5'-C4'). ; _item.name '_struct_mon_nucl.beta' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.chi1 _item_description.description ; The value in degrees of the sugar-base torsion angle chi1 (O4'-C1'-N1-C2). ; _item.name '_struct_mon_nucl.chi1' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.chi2 _item_description.description ; The value in degrees of the sugar-base torsion angle chi2 (O4'-C1'-N9-C4). ; _item.name '_struct_mon_nucl.chi2' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.delta _item_description.description ; The value in degrees of the backbone torsion angle delta (C5'-C4'-C3'-O3'). ; _item.name '_struct_mon_nucl.delta' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.details _item_description.description ; A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. ; _item.name '_struct_mon_nucl.details' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_examples.case ; Part of the phosphodiester backbone not in density. ; save_ save__struct_mon_nucl.epsilon _item_description.description ; The value in degrees of the backbone torsion angle epsilon (C4'-C3'-O3'-P). ; _item.name '_struct_mon_nucl.epsilon' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.gamma _item_description.description ; The value in degrees of the backbone torsion angle gamma (O5'-C5'-C4'-C3'). ; _item.name '_struct_mon_nucl.gamma' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.label_alt_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_mon_nucl.label_alt_id' _item.mandatory_code yes save_ save__struct_mon_nucl.label_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.label_asym_id' _item.mandatory_code yes save_ save__struct_mon_nucl.label_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.label_comp_id' _item.mandatory_code yes save_ save__struct_mon_nucl.label_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.label_seq_id' _item.mandatory_code yes save_ save__struct_mon_nucl.mean_B_all _item_description.description ; The mean value of the isotropic displacement parameter for all atoms in the monomer. ; _item.name '_struct_mon_nucl.mean_B_all' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.mean_B_base _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the base moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_base' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.mean_B_phos _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the phosphate moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_phos' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.mean_B_sugar _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the sugar moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_sugar' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.nu0 _item_description.description ; The value in degrees of the sugar torsion angle nu0 (C4'-O4'-C1'-C2'). ; _item.name '_struct_mon_nucl.nu0' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu1 _item_description.description ; The value in degrees of the sugar torsion angle nu1 (O4'-C1'-C2'-C3'). ; _item.name '_struct_mon_nucl.nu1' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu2 _item_description.description ; The value in degrees of the sugar torsion angle nu2 (C1'-C2'-C3'-C4'). ; _item.name '_struct_mon_nucl.nu2' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu3 _item_description.description ; The value in degrees of the sugar torsion angle nu3 (C2'-C3'-C4'-O4'). ; _item.name '_struct_mon_nucl.nu3' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu4 _item_description.description ; The value in degrees of the sugar torsion angle nu4 (C3'-C4'-O4'-C1'). ; _item.name '_struct_mon_nucl.nu4' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.P _item_description.description ; P is the phase angle of pseudorotation for five-membered rings. For ribose and deoxyribose sugars in nucleic acids (tau4 +tau1)-(tau3+tau0) P = ATAN (-------------------------) 2tau2 (sin 36+sin 72) If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam, 1972). Ref: Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212. ; _item.name '_struct_mon_nucl.P' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.RSCC_all _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_all' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSCC_base _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_base' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSCC_phos _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_phos' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSCC_sugar _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_sugar' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_all _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_all' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_base _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_base' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_phos _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_phos' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_sugar _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_sugar' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.tau0 _item_description.description ; The value in degrees of the sugar torsion angle tau0 (C4'-O4'-C1'-C2'). ; _item.name '_struct_mon_nucl.tau0' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau1 _item_description.description ; The value in degrees of the sugar torsion angle tau1 (O4'-C1'-C2'-C3'). ; _item.name '_struct_mon_nucl.tau1' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau2 _item_description.description ; The value in degrees of the sugar torsion angle tau2 (C1'-C2'-C3'-C4'). ; _item.name '_struct_mon_nucl.tau2' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau3 _item_description.description ; The value in degrees of the sugar torsion angle tau3 (C2'-C3'-C4'-O4'). ; _item.name '_struct_mon_nucl.tau3' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau4 _item_description.description ; The value in degrees of the sugar torsion angle tau4 (C3'-C4'-O4'-C1'). ; _item.name '_struct_mon_nucl.tau4' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.taum _item_description.description ; The maximum amplitude of puckering. This is derived from the pseudorotation value P and the torsion angles in the ribose ring. Tau2= Taum cosP Tau3= Taum cos(P+144) Tau4= Taum cos(P+288) Tau0= Taum cos(P+ 72) Tau1= Taum cos(P+216) ; _item.name '_struct_mon_nucl.taum' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.zeta _item_description.description ; The value in degrees of the backbone torsion angle zeta (C3'-O3'-P-O5'). ; _item.name '_struct_mon_nucl.zeta' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ ##################### ## STRUCT_MON_PROT ## ##################### save_struct_mon_prot _category.description ; Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. ; _category.id struct_mon_prot _category.mandatory_code no loop_ _category_key.name '_struct_mon_prot.label_alt_id' '_struct_mon_prot.label_asym_id' '_struct_mon_prot.label_comp_id' '_struct_mon_prot.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for protein NS1. This example provides details for residue ARG 35. ; ; _struct_mon_prot.label_comp_id ARG _struct_mon_prot.label_seq_id 35 _struct_mon_prot.label_asym_id A _struct_mon_prot.label_alt_id . _struct_mon_prot.chi1 -67.9 _struct_mon_prot.chi2 -174.7 _struct_mon_prot.chi3 -67.7 _struct_mon_prot.chi4 -86.3 _struct_mon_prot.chi5 4.2 _struct_mon_prot.RSCC_all 0.90 _struct_mon_prot.RSR_all 0.18 _struct_mon_prot.mean_B_all 30.0 _struct_mon_prot.mean_B_main 25.0 _struct_mon_prot.mean_B_side 35.1 _struct_mon_prot.omega 180.1 _struct_mon_prot.phi -60.3 _struct_mon_prot.psi -46.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_mon_prot.chi1 _item_description.description ; The value in degrees of the side-chain torsion angle chi1, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi1' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi2 _item_description.description ; The value in degrees of the side-chain torsion angle chi2, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi2' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi3 _item_description.description ; The value in degrees of the side-chain torsion angle chi3, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi3' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi4 _item_description.description ; The value in degrees of the side-chain torsion angle chi4, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi4' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi5 _item_description.description ; The value in degrees of the side-chain torsion angle chi5, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi5' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.details _item_description.description ; A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. ; _item.name '_struct_mon_prot.details' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float loop_ _item_examples.case 'very poor density' ; The side chain of this density may occupy alternative conformations, but alternative conformations were not fit in this model. ; ; This residue has a close contact with the bound inhibitor, which may account for the nonstandard conformation of the side chain. ; save_ save__struct_mon_prot.label_alt_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_mon_prot.label_alt_id' _item.mandatory_code yes save_ save__struct_mon_prot.label_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.label_asym_id' _item.mandatory_code yes save_ save__struct_mon_prot.label_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.label_comp_id' _item.mandatory_code yes save_ save__struct_mon_prot.label_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.label_seq_id' _item.mandatory_code yes save_ save__struct_mon_prot.auth_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.auth_asym_id' _item.mandatory_code no save_ save__struct_mon_prot.auth_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.auth_comp_id' _item.mandatory_code no save_ save__struct_mon_prot.auth_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.auth_seq_id' _item.mandatory_code no save_ save__struct_mon_prot.RSCC_all _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_prot.RSCC_all' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSCC_main _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_prot.RSCC_main' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSCC_side _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_prot.RSCC_side' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSR_all _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_prot.RSR_all' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSR_main _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_prot.RSR_main' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSR_side _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_prot.RSR_side' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.mean_B_all _item_description.description ; The mean value of the isotropic displacement parameter for all atoms in the monomer. ; _item.name '_struct_mon_prot.mean_B_all' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.mean_B_main _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the main chain of the monomer. ; _item.name '_struct_mon_prot.mean_B_main' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.mean_B_side _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the side chain of the monomer. ; _item.name '_struct_mon_prot.mean_B_side' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.omega _item_description.description ; The value in degrees of the main-chain torsion angle omega. ; _item.name '_struct_mon_prot.omega' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.phi _item_description.description ; The value in degrees of the main-chain torsion angle phi. ; _item.name '_struct_mon_prot.phi' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.psi _item_description.description ; The value in degrees of the main-chain torsion angle psi. ; _item.name '_struct_mon_prot.psi' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ ######################### ## STRUCT_MON_PROT_CIS ## ######################### save_struct_mon_prot_cis _category.description ; Data items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in _struct_mon_details.prot_cis. ; _category.id struct_mon_prot_cis _category.mandatory_code no loop_ _category_key.name '_struct_mon_prot_cis.label_alt_id' '_struct_mon_prot_cis.label_asym_id' '_struct_mon_prot_cis.label_comp_id' '_struct_mon_prot_cis.label_seq_id' '_struct_mon_prot_cis.pdbx_PDB_model_num' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield, Profy & Wilson [Science (1994), 264, 82-85]. ; ; loop_ _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_model_num PRO 8 L . 1 PRO 77 L . 1 PRO 95 L . 1 PRO 141 L . 1 # ----- abbreviated ----- ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_mon_prot_cis.label_alt_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_mon_prot_cis.label_alt_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.label_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.label_asym_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.label_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.label_comp_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.label_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.label_seq_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.auth_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.auth_asym_id' _item.mandatory_code no save_ save__struct_mon_prot_cis.auth_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.auth_comp_id' _item.mandatory_code no save_ save__struct_mon_prot_cis.auth_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.auth_seq_id' _item.mandatory_code no save_ #################### ## STRUCT_NCS_DOM ## #################### save_struct_ncs_dom _category.description ; Data items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators. A domain need not correspond to a complete polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain. ; _category.id struct_ncs_dom _category.mandatory_code no _category_key.name '_struct_ncs_dom.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; loop_ _struct_ncs_dom.id _struct_ncs_dom.details d1 'Chains A, B, and C' d2 'Chains D, E, and F' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_dom.details _item_description.description ; A description of special aspects of the structural elements that comprise a domain in an ensemble of domains related by noncrystallographic symmetry. ; _item.name '_struct_ncs_dom.details' _item.category_id struct_ncs_dom _item.mandatory_code no _item_type.code text _item_examples.case ; The loop between residues 18 and 23 in this domain interacts with a symmetry-related molecule, and thus deviates significantly from the noncrystallographic threefold. ; save_ save__struct_ncs_dom.id _item_description.description ; The value of _struct_ncs_dom.id must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_dom.id' struct_ncs_dom yes '_struct_ncs_dom_lim.dom_id' struct_ncs_dom_lim yes '_struct_ncs_ens_gen.dom_id_1' struct_ncs_ens_gen yes '_struct_ncs_ens_gen.dom_id_2' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_dom_lim.dom_id' '_struct_ncs_dom.id' '_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_dom.id' '_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_dom.id' _item_type.code code save_ ######################## ## STRUCT_NCS_DOM_LIM ## ######################## save_struct_ncs_dom_lim _category.description ; Data items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry. ; _category.id struct_ncs_dom_lim _category.mandatory_code no loop_ _category_key.name '_struct_ncs_dom_lim.dom_id' '_struct_ncs_dom_lim.beg_label_alt_id' '_struct_ncs_dom_lim.beg_label_asym_id' '_struct_ncs_dom_lim.beg_label_comp_id' '_struct_ncs_dom_lim.beg_label_seq_id' '_struct_ncs_dom_lim.end_label_alt_id' '_struct_ncs_dom_lim.end_label_asym_id' '_struct_ncs_dom_lim.end_label_comp_id' '_struct_ncs_dom_lim.end_label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; loop_ _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id d1 . A PRO 1 . A GLY 29 d1 . B PRO 31 . B GLY 59 d1 . C PRO 61 . B GLY 89 d2 . D PRO 91 . D GLY 119 d2 . E PRO 121 . E GLY 149 d2 . F PRO 151 . F GLY 179 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_dom_lim.beg_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_ncs_dom_lim.beg_label_alt_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_label_asym_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_label_comp_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_label_seq_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_auth_asym_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.beg_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_auth_comp_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.beg_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_auth_seq_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.dom_id _item_description.description ; This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_struct_ncs_dom_lim.dom_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_ncs_dom_lim.end_label_alt_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_label_asym_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_label_comp_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_label_seq_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_auth_asym_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.end_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_auth_comp_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.end_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_auth_seq_id' _item.mandatory_code no save_ #################### ## STRUCT_NCS_ENS ## #################### save_struct_ncs_ens _category.description ; Data items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry. The point group of the ensemble when taken as a whole may be specified, as well as any special aspects of the ensemble that require description. ; _category.id struct_ncs_ens _category.mandatory_code no _category_key.name '_struct_ncs_ens.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; _struct_ncs_ens.id en1 _struct_ncs_ens.details ; The ensemble represents the pseudo-twofold symmetry between domains d1 and d2. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_ens.details _item_description.description ; A description of special aspects of the ensemble. ; _item.name '_struct_ncs_ens.details' _item.category_id struct_ncs_ens _item.mandatory_code no _item_type.code text _item_examples.case ; The ensemble has a slight translation between domains 1 and 4, but overall it can accurately be described as point group 222 ; save_ save__struct_ncs_ens.id _item_description.description ; The value of _struct_ncs_ens.id must uniquely identify a record in the STRUCT_NCS_ENS list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_ens.id' struct_ncs_ens yes '_struct_ncs_ens_gen.ens_id' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.ens_id' '_struct_ncs_ens.id' _item_type.code code save_ save__struct_ncs_ens.point_group _item_description.description ; The point group of the ensemble of structural elements related by one or more noncrystallographic symmetry operations. The relationships need not be precise; this data item is intended to give a rough description of the noncrystallographic symmetry relationships. ; _item.name '_struct_ncs_ens.point_group' _item.category_id struct_ncs_ens _item.mandatory_code no _item_type.code line loop_ _item_examples.case '3' '422' 'non-proper' save_ ######################## ## STRUCT_NCS_ENS_GEN ## ######################## save_struct_ncs_ens_gen _category.description ; Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator. ; _category.id struct_ncs_ens_gen _category.mandatory_code no loop_ _category_key.name '_struct_ncs_ens_gen.ens_id' '_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_ens_gen.oper_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; _struct_ncs_ens_gen.dom_id_1 d1 _struct_ncs_ens_gen.dom_id_2 d2 _struct_ncs_ens_gen.ens_id en1 _struct_ncs_ens_gen.oper_id ncsop1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_ens_gen.dom_id_1 _item_description.description ; The identifier for the domain that will remain unchanged by the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_struct_ncs_ens_gen.dom_id_1' _item.mandatory_code yes save_ save__struct_ncs_ens_gen.dom_id_2 _item_description.description ; The identifier for the domain that will be transformed by application of the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_struct_ncs_ens_gen.dom_id_2' _item.mandatory_code yes save_ save__struct_ncs_ens_gen.ens_id _item_description.description ; This data item is a pointer to _struct_ncs_ens.id in the STRUCT_NCS_ENS category. ; _item.name '_struct_ncs_ens_gen.ens_id' _item.mandatory_code yes save_ save__struct_ncs_ens_gen.oper_id _item_description.description ; This data item is a pointer to _struct_ncs_oper.id in the STRUCT_NCS_OPER category. ; _item.name '_struct_ncs_ens_gen.oper_id' _item.mandatory_code yes save_ ##################### ## STRUCT_NCS_OPER ## ##################### save_struct_ncs_oper _category.description ; Data items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations. Each operator is specified as a matrix and a subsequent translation vector. Operators need not represent proper rotations. ; _category.id struct_ncs_oper _category.mandatory_code no _category_key.name '_struct_ncs_oper.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the protein NS1. ; ; _struct_ncs_oper.id ncsop1 _struct_ncs_oper.code given _struct_ncs_oper.matrix[1][1] 0.247 _struct_ncs_oper.matrix[1][2] 0.935 _struct_ncs_oper.matrix[1][3] 0.256 _struct_ncs_oper.matrix[2][1] 0.929 _struct_ncs_oper.matrix[2][2] 0.153 _struct_ncs_oper.matrix[2][3] 0.337 _struct_ncs_oper.matrix[3][1] 0.276 _struct_ncs_oper.matrix[3][2] 0.321 _struct_ncs_oper.matrix[3][3] -0.906 _struct_ncs_oper.vector[1] -8.253 _struct_ncs_oper.vector[2] -11.743 _struct_ncs_oper.vector[3] -1.782 _struct_ncs_oper.details ; Matrix and translation vector for pseudo-twofold operation. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_oper.code _item_description.description ; A code to indicate whether this operator describes a relationship between coordinates all of which are given in the data block (in which case the value of code is 'given'), or whether the operator is used to generate new coordinates from those that are given in the data block (in which case the value of code is 'generate'). ; _item.name '_struct_ncs_oper.code' _item.category_id struct_ncs_oper _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail given ; operator relates coordinates given in the data block ; generate ; operator generates new coordinates from those given in the data block ; save_ save__struct_ncs_oper.details _item_description.description ; A description of special aspects of the noncrystallographic symmetry operator. ; _item.name '_struct_ncs_oper.details' _item.category_id struct_ncs_oper _item.mandatory_code no _item_type.code text _item_examples.case ; The operation is given as a precise threefold rotation, despite the fact the best rms fit between domain 1 and domain 2 yields a rotation of 119.7 degrees and a translation of 0.13 angstroms. ; save_ save__struct_ncs_oper.id _item_description.description ; The value of _struct_ncs_oper.id must uniquely identify a record in the STRUCT_NCS_OPER list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_oper.id' struct_ncs_oper yes '_struct_ncs_ens_gen.oper_id' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.oper_id' '_struct_ncs_oper.id' _item_type.code code save_ save__struct_ncs_oper.matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[1][1]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[1][2]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[1][3]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[2][1]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[2][2]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[2][3]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[3][1]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[3][2]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[3][3]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.vector[1] _item_description.description ; The [1] element of the three-element vector component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.vector[1]' _item.category_id struct_ncs_oper _item.mandatory_code no # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__struct_ncs_oper.vector[2] _item_description.description ; The [2] element of the three-element vector component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.vector[2]' _item.category_id struct_ncs_oper _item.mandatory_code no # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__struct_ncs_oper.vector[3] _item_description.description ; The [3] element of the three-element vector component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.vector[3]' _item.category_id struct_ncs_oper _item.mandatory_code no # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ################ ## STRUCT_REF ## ################ save_struct_ref _category.description ; Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item _struct_ref.seq_align is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of _struct_ref.seq_dif is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category. ; _category.id struct_ref _category.mandatory_code no _category_key.name '_struct_ref.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.biol_id _struct_ref.db_name _struct_ref.db_code _struct_ref.seq_align _struct_ref.seq_dif _struct_ref.details 1 1 . 'Genbank' '12345' 'entire' 'yes' . 2 . 2 'PDB' '1ABC' . . ; The structure of the closely related compound, isobutyryl-pepstatin (pepstatin A) in complex with rhizopuspepsin ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_ref.biol_id' _item.mandatory_code no save_ save__struct_ref.db_code _item_description.description ; The code for this entity or biological unit or for a closely related entity or biological unit in the named database. ; _item.name '_struct_ref.db_code' _item.category_id struct_ref _item.mandatory_code yes _item_type.code line loop_ _item_examples.case '1ABC' 'ABCDEF' save_ save__struct_ref.db_name _item_description.description ; The name of the database containing reference information about this entity or biological unit. ; _item.name '_struct_ref.db_name' _item.category_id struct_ref _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'PDB' 'CSD' 'Genbank' save_ save__struct_ref.details _item_description.description ; A description of special aspects of the relationship between the entity or biological unit described in the data block and that in the referenced database entry. ; _item.name '_struct_ref.details' _item.category_id struct_ref _item.mandatory_code no _item_type.code text save_ save__struct_ref.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_struct_ref.entity_id' _item.mandatory_code yes save_ save__struct_ref.id _item_description.description ; The value of _struct_ref.id must uniquely identify a record in the STRUCT_REF list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ref.id' struct_ref yes '_struct_ref_seq.ref_id' struct_ref_seq yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ref_seq.ref_id' '_struct_ref.id' _item_type.code code save_ save__struct_ref.seq_align _item_description.description ; A flag to indicate the scope of the alignment between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. 'entire' indicates that alignment spans the entire length of both sequences (although point differences may occur and can be annotated using the data items in the STRUCT_REF_SEQ_DIF category). 'partial' indicates a partial alignment. The region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. This data item may also take the value '.', indicating that the reference is not to a sequence. ; _item.name '_struct_ref.seq_align' _item.category_id struct_ref _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail complete 'alignment is complete' partial 'alignment is partial' . 'reference is not to a sequence' save_ save__struct_ref.seq_dif _item_description.description ; A flag to indicate the presence ('yes') or absence ('no') of point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. This data item may also take the value '.', indicating that the reference is not to a sequence. ; _item.name '_struct_ref.seq_dif' _item.category_id struct_ref _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'there are no point differences' n 'abbreviation for "no"' yes 'there are point difference' y 'abbreviation for "yes"' . 'reference is not to a sequence' save_ #################### ## STRUCT_REF_SEQ ## #################### save_struct_ref_seq _category.description ; Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry. ; _category.id struct_ref_seq _category.mandatory_code no _category_key.name '_struct_ref_seq.align_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on the sequence alignment of CHER from M. xantus (36 to 288) and CHER from S. typhimurium (18 to 276). ; ; _struct_ref_seq.align_id alg1 _struct_ref_seq.ref_id seqdb1 _struct_ref_seq.seq_align_beg 36 _struct_ref_seq.seq_align_end 288 _struct_ref_seq.db_align_beg 18 _struct_ref_seq.db_align_end 276 _struct_ref_seq.details ; The alignment contains 3 gaps larger than 2 residues ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref_seq.align_id _item_description.description ; The value of _struct_ref_seq.align_id must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ref_seq.align_id' struct_ref_seq yes '_struct_ref_seq_dif.align_id' struct_ref_seq_dif yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ref_seq_dif.align_id' '_struct_ref_seq.align_id' _item_type.code code save_ save__struct_ref_seq.db_align_beg _item_description.description ; The sequence position in the referenced database entry at which the alignment begins. ; _item.name '_struct_ref_seq.db_align_beg' _item.mandatory_code yes # loop_ # _item_range.maximum # _item_range.minimum . 1 # 1 1 _item_type.code int save_ save__struct_ref_seq.db_align_end _item_description.description ; The sequence position in the referenced database entry at which the alignment ends. ; _item.name '_struct_ref_seq.db_align_end' _item.mandatory_code yes # loop_ # _item_range.maximum # _item_range.minimum . 1 # 1 1 _item_type.code int save_ save__struct_ref_seq.details _item_description.description ; A description of special aspects of the sequence alignment. ; _item.name '_struct_ref_seq.details' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code text save_ save__struct_ref_seq.ref_id _item_description.description ; This data item is a pointer to _struct_ref.id in the STRUCT_REF category. ; _item.name '_struct_ref_seq.ref_id' _item.mandatory_code yes save_ save__struct_ref_seq.seq_align_beg _item_description.description ; The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq.seq_align_beg' _item.mandatory_code yes save_ save__struct_ref_seq.seq_align_end _item_description.description ; The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq.seq_align_end' _item.mandatory_code yes save_ ######################## ## STRUCT_REF_SEQ_DIF ## ######################## save_struct_ref_seq_dif _category.description ; Data items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry. ; _category.id struct_ref_seq_dif _category.mandatory_code no _category_key.name '_struct_ref_seq_dif.pdbx_ordinal' # # loop_ # _category_key.name '_struct_ref_seq_dif.align_id' # '_struct_ref_seq_dif.seq_num' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for CAP-DNA complex. ; ; _struct_ref_seq_dif.pdbx_ordinal 1 _struct_ref_seq_dif.align_id algn2 _struct_ref_seq_dif.seq_num 181 _struct_ref_seq_dif.db_mon_id GLU _struct_ref_seq_dif.mon_id PHE _struct_ref_seq_dif.details ; A point mutation was introduced in the CAP at position 181 substituting PHE for GLU. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref_seq_dif.align_id _item_description.description ; This data item is a pointer to _struct_ref_seq.align_id in the STRUCT_REF_SEQ category. ; _item.name '_struct_ref_seq_dif.align_id' _item.mandatory_code yes save_ save__struct_ref_seq_dif.db_mon_id _item_description.description ; The monomer type found at this position in the referenced database entry. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_ref_seq_dif.db_mon_id' _item.mandatory_code yes save_ save__struct_ref_seq_dif.details _item_description.description ; A description of special aspects of the point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. ; _item.name '_struct_ref_seq_dif.details' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code text save_ save__struct_ref_seq_dif.mon_id _item_description.description ; The monomer type found at this position in the sequence of the entity or biological unit described in this data block. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_ref_seq_dif.mon_id' _item.mandatory_code yes save_ save__struct_ref_seq_dif.seq_num _item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq_dif.seq_num' _item.mandatory_code yes save_ ################## ## STRUCT_SHEET ## ################## save_struct_sheet _category.description ; Data items in the STRUCT_SHEET category record details about the beta-sheets. ; _category.id struct_sheet _category.mandatory_code no _category_key.name '_struct_sheet.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. N O N O N O N O N O N O 10--11--12--13--14--15--16--17--18--19--20 strand_a N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 30--31--32--33--34--35--36--37--38--39--40 strand_b N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 50--51--52--53--54--55--56--57--58--59--60 strand_c N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 70--71--72--73--74--75--76--77--78--79--80 strand_d N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 90--91--92--93--94--95--96--97--98--99-100 strand_e N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 110-111-112-113-114-115-116-117-118-119-120 strand_f N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 130-131-132-133-134-135-136-137-138-139-140 strand_g N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 150-151-152-153-154-155-156-157-158-159-160 strand_h N O N O N O N O N O / \ / \ / \ / \ / \ ; ; _struct_sheet.id sheet_1 _struct_sheet.type 'beta-barrel' _struct_sheet.number_strands 8 _struct_sheet.details . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. N O N O N O N O -10--11--12--13--14--15--16--17--18-> strand_a N O N O N O N O N O | | | | | | | | | | O N O N O N O N O N <-119-118-117-116-115-114-113-112-111-110- strand_b O N O N O N O N O N \ / \ / \ / \ / \ O N O N O N O N O N O N <-41--40--39--38--37--36--35--34--33--32--31--30- strand_c O N O N O N O N O N O N | | | | | | | | | | | | N O N O N O N O N O N O strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2 N O N O N O N O N O | | | | | | | | | | | | O N O N O N O N O N O N <-80--79--78--77--76--75--74--73--72--71--70- strand_e O N O N O N O N O N ; ; _struct_sheet.id sheet_2 _struct_sheet.type 'five stranded, mixed-sense' _struct_sheet.number_strands 5 _struct_sheet.details 'strand_d is in two pieces' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet.details _item_description.description ; A description of special aspects of the beta-sheet. ; _item.name '_struct_sheet.details' _item.category_id struct_sheet _item.mandatory_code no _item_type.code text save_ save__struct_sheet.id _item_description.description ; The value of _struct_sheet.id must uniquely identify a record in the STRUCT_SHEET list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_sheet.id' struct_sheet yes '_struct_sheet_hbond.sheet_id' struct_sheet_hbond yes '_struct_sheet_order.sheet_id' struct_sheet_order yes '_struct_sheet_range.sheet_id' struct_sheet_range yes '_struct_sheet_topology.sheet_id' struct_sheet_topology yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_sheet_hbond.sheet_id' '_struct_sheet.id' '_struct_sheet_order.sheet_id' '_struct_sheet.id' '_struct_sheet_range.sheet_id' '_struct_sheet.id' '_struct_sheet_topology.sheet_id' '_struct_sheet.id' _item_type.code code save_ save__struct_sheet.number_strands _item_description.description ; The number of strands in the sheet. If a given range of residues bulges out from the strands, it is still counted as one strand. If a strand is composed of two different regions of polypeptide, it is still counted as one strand, as long as the proper hydrogen- bonding connections are made to adjacent strands. ; _item.name '_struct_sheet.number_strands' _item.category_id struct_sheet _item.mandatory_code no _item_type.code int save_ save__struct_sheet.type _item_description.description ; A simple descriptor for the type of the sheet. ; _item.name '_struct_sheet.type' _item.category_id struct_sheet _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'jelly-roll' 'Rossmann fold' 'beta barrel' save_ ######################## ## STRUCT_SHEET_HBOND ## ######################## save_struct_sheet_hbond _category.description ; Data items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet. It is necessary to treat hydrogen bonding independently of the designation of ranges, because the hydrogen bonding may begin in different places for the interactions of a given strand with the one preceding it and the one following it in the sheet. ; _category.id struct_sheet_hbond _category.mandatory_code no loop_ _category_key.name '_struct_sheet_hbond.sheet_id' '_struct_sheet_hbond.range_id_1' '_struct_sheet_hbond.range_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_hbond.sheet_id _struct_sheet_hbond.range_id_1 _struct_sheet_hbond.range_id_2 _struct_sheet_hbond.range_1_beg_label_seq_id _struct_sheet_hbond.range_1_beg_label_atom_id _struct_sheet_hbond.range_2_beg_label_seq_id _struct_sheet_hbond.range_2_beg_label_atom_id _struct_sheet_hbond.range_1_end_label_seq_id _struct_sheet_hbond.range_1_end_label_atom_id _struct_sheet_hbond.range_2_end_label_seq_id _struct_sheet_hbond.range_2_end_label_atom_id sheet_1 strand_a strand_b 11 N 30 O 19 O 40 N sheet_1 strand_b strand_c 31 N 50 O 39 O 60 N sheet_1 strand_c strand_d 51 N 70 O 59 O 80 N sheet_1 strand_d strand_e 71 N 90 O 89 O 100 N sheet_1 strand_e strand_f 91 N 110 O 99 O 120 N sheet_1 strand_f strand_g 111 N 130 O 119 O 140 N sheet_1 strand_g strand_h 131 N 150 O 139 O 160 N sheet_1 strand_h strand_a 151 N 10 O 159 O 180 N ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_hbond.sheet_id _struct_sheet_hbond.range_id_1 _struct_sheet_hbond.range_id_2 _struct_sheet_hbond.range_1_beg_label_seq_id _struct_sheet_hbond.range_1_beg_label_atom_id _struct_sheet_hbond.range_2_beg_label_seq_id _struct_sheet_hbond.range_2_beg_label_atom_id _struct_sheet_hbond.range_1_end_label_seq_id _struct_sheet_hbond.range_1_end_label_atom_id _struct_sheet_hbond.range_2_end_label_seq_id _struct_sheet_hbond.range_2_end_label_atom_id sheet_2 strand_a strand_b 20 N 119 O 18 O 111 N sheet_2 strand_b strand_c 110 N 33 O 118 N 41 O sheet_2 strand_c strand_d1 38 N 52 O 40 O 50 N sheet_2 strand_c strand_d2 30 N 96 O 36 O 90 N sheet_2 strand_d1 strand_e 51 N 80 O 51 O 80 N sheet_2 strand_d2 strand_e 91 N 76 O 97 O 70 N ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_hbond.range_1_beg_label_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_beg_label_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_end_label_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_end_label_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_beg_label_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_beg_label_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_end_label_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_end_label_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_beg_auth_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_1_beg_auth_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_1_end_auth_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_1_end_auth_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_beg_auth_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_beg_auth_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_end_auth_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_end_auth_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_id_1 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_hbond.range_id_1' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_id_2 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_hbond.range_id_2' _item.mandatory_code yes save_ save__struct_sheet_hbond.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_hbond.sheet_id' _item.mandatory_code yes save_ ######################## ## STRUCT_SHEET_ORDER ## ######################## save_struct_sheet_order _category.description ; Data items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet. These data items are an alternative to the STRUCT_SHEET_TOPOLOGY data items and they allow all manner of sheets to be described. ; _category.id struct_sheet_order _category.mandatory_code no loop_ _category_key.name '_struct_sheet_order.sheet_id' '_struct_sheet_order.range_id_1' '_struct_sheet_order.range_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense sheet_1 strand_a strand_b +1 parallel sheet_1 strand_b strand_c +1 parallel sheet_1 strand_c strand_d +1 parallel sheet_1 strand_d strand_e +1 parallel sheet_1 strand_e strand_f +1 parallel sheet_1 strand_f strand_g +1 parallel sheet_1 strand_g strand_h +1 parallel sheet_1 strand_h strand_a +1 parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense sheet_2 strand_a strand_b +1 anti-parallel sheet_2 strand_b strand_c +1 parallel sheet_2 strand_c strand_d1 +1 anti-parallel sheet_2 strand_c strand_d2 +1 anti-parallel sheet_2 strand_d1 strand_e +1 anti-parallel sheet_2 strand_d2 strand_e +1 anti-parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_order.offset _item_description.description ; Designates the relative position in the sheet, plus or minus, of the second residue range to the first. ; _item.name '_struct_sheet_order.offset' _item.category_id struct_sheet_order _item.mandatory_code no _item_type.code int save_ save__struct_sheet_order.range_id_1 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_order.range_id_1' _item.mandatory_code yes save_ save__struct_sheet_order.range_id_2 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_order.range_id_2' _item.mandatory_code yes save_ save__struct_sheet_order.sense _item_description.description ; A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. ; _item.name '_struct_sheet_order.sense' _item.category_id struct_sheet_order _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value 'parallel' 'anti-parallel' save_ save__struct_sheet_order.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_order.sheet_id' _item.mandatory_code yes save_ ######################## ## STRUCT_SHEET_RANGE ## ######################## save_struct_sheet_range _category.description ; Data items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet. Residues are included in a range if they made beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range. ; _category.id struct_sheet_range _category.mandatory_code no loop_ _category_key.name '_struct_sheet_range.sheet_id' '_struct_sheet_range.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.symmetry sheet_1 strand_a ala A 20 ala A 30 1_555 sheet_1 strand_b ala A 40 ala A 50 1_555 sheet_1 strand_c ala A 60 ala A 70 1_555 sheet_1 strand_d ala A 80 ala A 90 1_555 sheet_1 strand_e ala A 100 ala A 110 1_555 sheet_1 strand_f ala A 120 ala A 130 1_555 sheet_1 strand_g ala A 140 ala A 150 1_555 sheet_1 strand_h ala A 160 ala A 170 1_555 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.symmetry sheet_2 strand_a ala A 10 ala A 18 1_555 sheet_2 strand_b ala A 110 ala A 119 1_555 sheet_2 strand_c ala A 30 ala A 41 1_555 sheet_2 strand_d1 ala A 50 ala A 52 1_555 sheet_2 strand_d2 ala A 90 ala A 97 1_555 sheet_2 strand_e ala A 70 ala A 80 1_555 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_range.beg_label_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_struct_sheet_range.beg_label_asym_id' _item.mandatory_code yes save_ save__struct_sheet_range.beg_label_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_sheet_range.beg_label_comp_id' _item.mandatory_code yes save_ save__struct_sheet_range.beg_label_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_range.end_label_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_struct_sheet_range.end_label_asym_id' _item.mandatory_code yes save_ save__struct_sheet_range.end_label_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_sheet_range.end_label_comp_id' _item.mandatory_code yes save_ save__struct_sheet_range.end_label_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_range.beg_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_auth_asym_id' _item.mandatory_code no save_ save__struct_sheet_range.beg_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_auth_comp_id' _item.mandatory_code no save_ save__struct_sheet_range.beg_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_range.end_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_auth_asym_id' _item.mandatory_code no save_ save__struct_sheet_range.end_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_auth_comp_id' _item.mandatory_code no save_ save__struct_sheet_range.end_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_range.id _item_description.description ; The value of _struct_sheet_range.id must uniquely identify a range in a given sheet in the STRUCT_SHEET_RANGE list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_sheet_range.id' struct_sheet_range yes '_struct_sheet_hbond.range_id_1' struct_sheet_hbond yes '_struct_sheet_hbond.range_id_2' struct_sheet_hbond yes '_struct_sheet_order.range_id_1' struct_sheet_order yes '_struct_sheet_order.range_id_2' struct_sheet_order yes '_struct_sheet_topology.range_id_1' struct_sheet_topology yes '_struct_sheet_topology.range_id_2' struct_sheet_topology yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_sheet_hbond.range_id_1' '_struct_sheet_range.id' '_struct_sheet_hbond.range_id_2' '_struct_sheet_range.id' '_struct_sheet_order.range_id_1' '_struct_sheet_range.id' '_struct_sheet_order.range_id_2' '_struct_sheet_range.id' '_struct_sheet_topology.range_id_1' '_struct_sheet_range.id' '_struct_sheet_topology.range_id_2' '_struct_sheet_range.id' _item_type.code code save_ save__struct_sheet_range.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_range.sheet_id' _item.mandatory_code yes save_ save__struct_sheet_range.symmetry _item_description.description ; Describes the symmetry operation that should be applied to the residues delimited by the start and end designators in order to generate the appropriate strand in this sheet. ; _item.name '_struct_sheet_range.symmetry' _item.category_id struct_sheet_range _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop save_ ########################### ## STRUCT_SHEET_TOPOLOGY ## ########################### save_struct_sheet_topology _category.description ; Data items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet. All topology links are pairwise and the specified pairs are assumed to be successive in the amino-acid sequence. These data items are useful in describing various simple and complex folds, but they become inadequate when the strands in the sheet come from more than one chain. The STRUCT_SHEET_ORDER data items can be used to describe single- and multiple-chain-containing sheets. ; _category.id struct_sheet_topology _category.mandatory_code no loop_ _category_key.name '_struct_sheet_topology.sheet_id' '_struct_sheet_topology.range_id_1' '_struct_sheet_topology.range_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_topology.sheet_id _struct_sheet_topology.range_id_1 _struct_sheet_topology.range_id_2 _struct_sheet_topology.offset _struct_sheet_topology.sense sheet_1 strand_a strand_b +1 parallel sheet_1 strand_b strand_c +1 parallel sheet_1 strand_c strand_d +1 parallel sheet_1 strand_d strand_e +1 parallel sheet_1 strand_e strand_f +1 parallel sheet_1 strand_f strand_g +1 parallel sheet_1 strand_g strand_h +1 parallel sheet_1 strand_h strand_a +1 parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_topology.sheet_id _struct_sheet_topology.range_id_1 _struct_sheet_topology.range_id_2 _struct_sheet_topology.offset _struct_sheet_topology.sense sheet_2 strand_a strand_c +2 anti-parallel sheet_2 strand_c strand_d1 +1 anti-parallel sheet_2 strand_d1 strand_e +1 anti-parallel sheet_2 strand_e strand_d2 -1 anti-parallel sheet_2 strand_d2 strand_b -2 anti-parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_topology.offset _item_description.description ; Designates the relative position in the sheet, plus or minus, of the second residue range to the first. ; _item.name '_struct_sheet_topology.offset' _item.category_id struct_sheet_topology _item.mandatory_code no _item_type.code int save_ save__struct_sheet_topology.range_id_1 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_topology.range_id_1' _item.mandatory_code yes save_ save__struct_sheet_topology.range_id_2 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_topology.range_id_2' _item.mandatory_code yes save_ save__struct_sheet_topology.sense _item_description.description ; A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. ; _item.name '_struct_sheet_topology.sense' _item.category_id struct_sheet_topology _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value 'parallel' 'anti-parallel' save_ save__struct_sheet_topology.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_topology.sheet_id' _item.mandatory_code yes save_ ################# ## STRUCT_SITE ## ################# save_struct_site _category.description ; Data items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g. active sites, substrate-binding subsites, metal-coordination sites). ; _category.id struct_site _category.mandatory_code no _category_key.name '_struct_site.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_site.id _struct_site.details 'P2 site C' ; residues with a contact < 3.7 \%A to an atom in the P2 moiety of the inhibitor in the conformation with _struct_asym.id = C ; 'P2 site D' ; residues with a contact < 3.7 \%A to an atom in the P1 moiety of the inhibitor in the conformation with _struct_asym.id = D) ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site.details _item_description.description ; A description of special aspects of the site. ; _item.name '_struct_site.details' _item.category_id struct_site _item.mandatory_code no _item_type.code text save_ save__struct_site.id _item_description.description ; The value of _struct_site.id must uniquely identify a record in the STRUCT_SITE list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_site.id' struct_site yes '_struct_site_gen.site_id' struct_site_gen yes '_struct_site_keywords.site_id' struct_site_keywords yes '_struct_site_view.site_id' struct_site_view yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_site_gen.site_id' '_struct_site.id' '_struct_site_keywords.site_id' '_struct_site.id' '_struct_site_view.site_id' '_struct_site.id' _item_type.code line save_ ##################### ## STRUCT_SITE_GEN ## ##################### save_struct_site_gen _category.description ; Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites. ; _category.id struct_site_gen _category.mandatory_code no loop_ _category_key.name '_struct_site_gen.id' '_struct_site_gen.site_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.symmetry _struct_site_gen.details 1 1 VAL A 32 1_555 . 2 1 ILE A 47 1_555 . 3 1 VAL A 82 1_555 . 4 1 ILE A 84 1_555 . 5 2 VAL B 232 1_555 . 6 2 ILE B 247 1_555 . 7 2 VAL B 282 1_555 . 8 2 ILE B 284 1_555 . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site_gen.details _item_description.description ; A description of special aspects of the symmetry generation of this portion of the structural site. ; _item.name '_struct_site_gen.details' _item.category_id struct_site_gen _item.mandatory_code no _item_type.code text _item_examples.case ; The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. ; save_ save__struct_site_gen.id _item_description.description ; The value of _struct_site_gen.id must uniquely identify a record in the STRUCT_SITE_GEN list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_site_gen.id' _item.category_id struct_site_gen _item.mandatory_code yes _item_type.code line save_ save__struct_site_gen.label_alt_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_site_gen.label_alt_id' _item.mandatory_code yes save_ save__struct_site_gen.label_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.label_asym_id' _item.mandatory_code yes save_ save__struct_site_gen.label_atom_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_struct_site_gen.label_atom_id' _item.mandatory_code yes save_ save__struct_site_gen.label_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.label_comp_id' _item.mandatory_code yes save_ save__struct_site_gen.label_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.label_seq_id' _item.mandatory_code yes save_ save__struct_site_gen.auth_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_asym_id' _item.mandatory_code no save_ save__struct_site_gen.auth_atom_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_atom_id' _item.mandatory_code no save_ save__struct_site_gen.auth_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_comp_id' _item.mandatory_code no save_ save__struct_site_gen.auth_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_seq_id' _item.mandatory_code no save_ save__struct_site_gen.site_id _item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ; _item.name '_struct_site_gen.site_id' _item.mandatory_code yes save_ save__struct_site_gen.symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_site_gen.label* to generate a portion of the site. ; _item.name '_struct_site_gen.symmetry' _item.category_id struct_site_gen _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ########################## ## STRUCT_SITE_KEYWORDS ## ########################## save_struct_site_keywords _category.description ; Data items in the STRUCT_SITE_KEYWORDS category record keywords describing the site. ; _category.id struct_site_keywords _category.mandatory_code no loop_ _category_key.name '_struct_site_keywords.site_id' '_struct_site_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_site_keywords.site_id _struct_site_keywords.text 'P2 site C' 'binding site' 'P2 site C' 'binding pocket' 'P2 site C' 'P2 site' 'P2 site C' 'P2 pocket' 'P2 site D' 'binding site' 'P2 site D' 'binding pocket' 'P2 site D' 'P2 site' 'P2 site D' 'P2 pocket' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site_keywords.site_id _item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ; _item.name '_struct_site_keywords.site_id' _item.mandatory_code yes save_ save__struct_site_keywords.text _item_description.description ; Keywords describing this site. ; _item.name '_struct_site_keywords.text' _item.category_id struct_site_keywords _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'active site' 'binding pocket' 'Ca coordination' save_ ###################### ## STRUCT_SITE_VIEW ## ###################### save_struct_site_view _category.description ; Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site. ; _category.id struct_site_view _category.mandatory_code no _category_key.name '_struct_site_view.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry (1989), 28, 310-320]. ; ; _struct_site_view.id 1 _struct_site_view.rot_matrix[1][1] 0.132 _struct_site_view.rot_matrix[1][2] 0.922 _struct_site_view.rot_matrix[1][3] -0.363 _struct_site_view.rot_matrix[2][1] 0.131 _struct_site_view.rot_matrix[2][2] -0.380 _struct_site_view.rot_matrix[2][3] -0.916 _struct_site_view.rot_matrix[3][1] -0.982 _struct_site_view.rot_matrix[3][2] 0.073 _struct_site_view.rot_matrix[3][3] -0.172 _struct_site_view.details ; This view highlights the site of ATAT-Netropsin interaction. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site_view.details _item_description.description ; A description of special aspects of this view of the site. This data item can be used as a figure legend. ; _item.name '_struct_site_view.details' _item.category_id struct_site_view _item.mandatory_code no _item_type.code text _item_examples.case ; The active site has been oriented with the specificity pocket on the right and the active site machinery on the left. ; save_ save__struct_site_view.id _item_description.description ; The value of _struct_site_view.id must uniquely identify a record in the STRUCT_SITE_VIEW list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_site_view.id' _item.category_id struct_site_view _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Figure 1' 'unliganded enzyme' 'view down enzyme active site' save_ save__struct_site_view.rot_matrix[1][1] _item_description.description ; The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[1][1]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[1][2] _item_description.description ; The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[1][2]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[1][3] _item_description.description ; The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[1][3]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[2][1] _item_description.description ; The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[2][1]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[2][2] _item_description.description ; The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[2][2]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[2][3] _item_description.description ; The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[2][3]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[3][1] _item_description.description ; The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[3][1]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[3][2] _item_description.description ; The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[3][2]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[3][3] _item_description.description ; The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[3][3]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.site_id _item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ; _item.name '_struct_site_view.site_id' _item.mandatory_code yes save_ ############## ## SYMMETRY ## ############## save_symmetry _category.description ; Data items in the SYMMETRY category record details about the space-group symmetry. ; _category.id symmetry _category.mandatory_code no _category_key.name '_symmetry.entry_id' loop_ _category_group.id 'inclusive_group' 'symmetry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _symmetry.entry_id '5HVP' _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 18 _symmetry.space_group_name_H-M 'P 21 21 2' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__symmetry.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_symmetry.entry_id' _item.mandatory_code yes save_ save__symmetry.cell_setting _item_description.description ; The cell settings for this space-group symmetry. ; _item.name '_symmetry.cell_setting' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_cell_setting' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value triclinic monoclinic orthorhombic tetragonal rhombohedral trigonal hexagonal cubic save_ save__symmetry.Int_Tables_number _item_description.description ; Space-group number from International Tables for Crystallography Vol. A (2002). ; _item.name '_symmetry.Int_Tables_number' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_Int_Tables_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__symmetry.space_group_name_Hall _item_description.description ; Space-group symbol as described by Hall (1981). This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981) A37, 921. ; _item.name '_symmetry.space_group_name_Hall' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_space_group_name_Hall' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '-P 2ac 2n' '-R 3 2"' 'P 61 2 2 (0 0 -1)' save_ save__symmetry.space_group_name_H-M _item_description.description ; Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the _symmetry_equiv.pos_as_xyz or _symmetry.space_group_name_Hall data items as well. Leave spaces between symbols referring to different axes. ; _item.name '_symmetry.space_group_name_H-M' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_space_group_name_H-M' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'P 1 21/m 1' 'P 2/n 2/n 2/n (origin at -1)' 'R -3 2/m' save_ #################### ## SYMMETRY_EQUIV ## #################### save_symmetry_equiv _category.description ; Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group. ; _category.id symmetry_equiv _category.mandatory_code no _category_key.name '_symmetry_equiv.id' loop_ _category_group.id 'inclusive_group' 'symmetry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 '+x,+y,+z' 2 '-x,-y,z' 3 '1/2+x,1/2-y,-z' 4 '1/2-x,1/2+y,-z' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__symmetry_equiv.id _item_description.description ; The value of _symmetry_equiv.id must uniquely identify a record in the SYMMETRY_EQUIV category. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_symmetry_equiv.id' _item.category_id symmetry_equiv _item.mandatory_code yes _item_aliases.alias_name '_symmetry_equiv_pos_site_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__symmetry_equiv.pos_as_xyz _item_description.description ; Symmetry-equivalent position in the 'xyz' representation. Except for the space group P1, these data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography Vol. A (2002). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present. ; _item.name '_symmetry_equiv.pos_as_xyz' _item.category_id symmetry_equiv _item.mandatory_code no _item_aliases.alias_name '_symmetry_equiv_pos_as_xyz' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '-y+x,-y,1/3+z' save_ ### EOF mmcif_std-def-1.dic ########################################################################### # # File: mmcif_std-def-2.dic # # mmCIF Data Dictionary # # This data dictionary contains the standard mmCIF data definitions. # # Defintion Section 2 # # Section 2 contains definitions added to maintain correspondence # with the Core CIF dictionary V2.3 # # # ########################################################################### save__atom_site.adp_type _item_description.description ; A standard code used to describe the type of atomic displacement parameters used for the site. ; _item.name '_atom_site.adp_type' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.thermal_displace_type' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_adp_type' cif_core.dic 2.3 save_ save__atom_site.refinement_flags _item_description.description ; A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by _atom_site.refinement_flags_posn, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with old CIFs. ; _item.name '_atom_site.refinement_flags' _item.category_id atom_site _item.mandatory_code no _item_type.code code loop_ _item_related.related_name _item_related.function_code '_atom_site.refinement_flags_posn' replaces '_atom_site.refinement_flags_adp' replaces '_atom_site.refinement_flags_occupancy' replaces loop_ _item_enumeration.value _item_enumeration.detail . 'no refinement constraints' S 'special-position constraint on site' G 'rigid-group refinement of site' R 'riding-atom site attached to non-riding atom' D 'distance or angle restraint on site' T 'thermal displacement constraints' U 'Uiso or Uij restraint (rigid bond)' P 'partial occupancy constraint' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags' cif_core.dic 2.3 save_ save__atom_site.refinement_flags_adp _item_description.description ; A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site. ; _item.name '_atom_site.refinement_flags_adp' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.refinement_flags_posn' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail . 'no constraints on atomic displacement parameters' T 'special-position constraints on atomic displacement parameters' U 'Uiso or Uij restraint (rigid bond)' TU 'both constraints applied' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags_adp' cif_core.dic 2.3 save_ save__atom_site.refinement_flags_occupancy _item_description.description ; A code which indicates that refinement restraints or constraints were applied to the occupancy of this site. ; _item.name '_atom_site.refinement_flags_occupancy' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.refinement_flags_posn' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail . 'no constraints on site-occupancy parameters' P 'site-occupancy constraint' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags_occupancy' cif_core.dic 2.3 save_ save__atom_site.refinement_flags_posn _item_description.description ; A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site. ; _item.name '_atom_site.refinement_flags_posn' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.refinement_flags_posn' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail . 'no constraints on positional coordinates' D 'distance or angle restraint on positional coordinates' G 'rigid-group refinement of positional coordinates' R 'riding-atom site attached to non-riding atom' S 'special-position constraint on positional coordinates' DG 'combination of the above constraints' DR 'combination of the above constraints' DS 'combination of the above constraints' GR 'combination of the above constraints' GS 'combination of the above constraints' RS 'combination of the above constraints' DGR 'combination of the above constraints' DGS 'combination of the above constraints' DRS 'combination of the above constraints' GRS 'combination of the above constraints' DGRS 'combination of the above constraints' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags_posn' cif_core.dic 2.3 save_ save__atom_sites.special_details _item_description.description ; Additional information about the atomic coordinates not coded elsewhere in the CIF. ; _item.name '_atom_sites.special_details' _item.category_id atom_sites _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_sites_special_details' cif_core.dic 2.3 save_ save__atom_type.scat_dispersion_source _item_description.description ; Reference to the source of the real and imaginary dispersion corrections for scattering factors used for this atom type. ; _item.name '_atom_type.scat_dispersion_source' _item.category_id atom_type _item.mandatory_code no _item_type.code text _item_examples.case 'International Tables Vol. IV Table 2.3.1' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_type_scat_dispersion_source' cif_core.dic 2.3 save_ ################ ## AUDIT_LINK ## ################ save_audit_link _category.description ; Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF. ; _category.id 'audit_link' _category.mandatory_code no loop_ _category_key.name '_audit_link.block_code' '_audit_link.block_description' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_link.block_code _audit_link.block_description . 'discursive text of paper with two structures' morA_(1) 'structure 1 of 2' morA_(2) 'structure 2 of 2' ; ; Example 1 - multiple structure paper, as illustrated in A Guide to CIF for Authors (1995). IUCr: Chester. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_link.block_code _audit_link.block_description . 'publication details' KSE_COM 'experimental data common to ref./mod. structures' KSE_REF 'reference structure' KSE_MOD 'modulated structure' ; ; Example 2 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_link.block_code _item_description.description ; The value of _audit_block.code associated with a data block in the current file related to the current data block. The special value '.' may be used to refer to the current data block for completeness. ; _item.name '_audit_link.block_code' _item.category_id audit_link _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_audit_link_block_code' cif_core.dic 2.3 save_ save__audit_link.block_description _item_description.description ; A textual description of the relationship of the referenced data block to the current one. ; _item.name '_audit_link.block_description' _item.category_id audit_link _item.mandatory_code yes _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_audit_link_block_description' cif_core.dic 2.3 save_ ## save__cell.reciprocal_angle_alpha _item_description.description ; The angle (recip-alpha) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_angle_alpha' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 180.0 180.0 180.0 _item_default.value 90.0 _item_type_conditions.code esd _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_alpha_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_angle_alpha' cif_core.dic 2.3 save_ save__cell.reciprocal_angle_beta _item_description.description ; The angle (recip-beta) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_angle_beta' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 180.0 180.0 180.0 _item_default.value 90.0 _item_type_conditions.code esd _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_beta_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_angle_beta' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_gamma _item_description.description ; The angle (recip-gamma) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_angle_gamma' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 180.0 180.0 180.0 _item_default.value 90.0 _item_type_conditions.code esd _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_gamma_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_angle_gamma' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_alpha_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_angle_alpha. ; _item.name '_cell.reciprocal_angle_alpha_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_alpha' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_angle_alpha_esd' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_beta_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_angle_beta. ; _item.name '_cell.reciprocal_angle_beta_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_beta' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_angle_beta_esd' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_gamma_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_angle_gamma. ; _item.name '_cell.reciprocal_angle_gamma_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_gamma' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_angle_gamma_esd' cif_core.dic 2.3 save_ # save__cell.reciprocal_length_a _item_description.description ; The reciprocal cell length (recip-a) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_length_a' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'reciprocal_angstroms' _item_type_conditions.code esd _item_related.related_name '_cell.reciprocal_length_a_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_length_a' cif_core.dic 2.3 save_ save__cell.reciprocal_length_b _item_description.description ; The reciprocal cell length (recip-b) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_length_b' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'reciprocal_angstroms' _item_type_conditions.code esd _item_related.related_name '_cell.reciprocal_length_b_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_length_b' cif_core.dic 2.3 save_ save__cell.reciprocal_length_c _item_description.description ; The reciprocal cell length (recip-c) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_length_c' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'reciprocal_angstroms' _item_type_conditions.code esd _item_related.related_name '_cell.reciprocal_length_c_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_length_c' cif_core.dic 2.3 save_ save__cell.reciprocal_length_a_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_length_a. ; _item.name '_cell.reciprocal_length_a_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'reciprocal_angstroms' _item_related.related_name '_cell.reciprocal_length_a' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_length_a_esd' cif_core.dic 2.3 save_ save__cell.reciprocal_length_b_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_length_b. ; _item.name '_cell.reciprocal_length_b_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'reciprocal_angstroms' _item_related.related_name '_cell.reciprocal_length_b' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_length_b_esd' cif_core.dic 2.3 save_ save__cell.reciprocal_length_c_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_length_c. ; _item.name '_cell.reciprocal_length_c_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'reciprocal_angstroms' _item_related.related_name '_cell.reciprocal_length_c' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_length_c_esd' cif_core.dic 2.3 save_ # save__cell.special_details # _item_description.description # ; A description of special aspects of the cell choice, noting # possible alternative settings. # ; # _item.name '_cell.special_details' # _item.category_id cell # _item.mandatory_code no # _item_type.code text # loop_ # _item_examples.case # 'pseudo-orthorhombic' # 'standard setting from 45 deg rotation around c' # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_special_details' cif_core.dic 2.3 # save_ # # save__chemical.absolute_configuration _item_description.description ; Necessary conditions for the assignment of _chemical.absolute_configuration are given by H. D. Flack and G. Bernardinelli (1999, 2000). Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. (http://www.iucr.org/paper?sh0129) Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. (http://www.iucr.org/paper?ks0021) ; _item.name '_chemical.absolute_configuration' _item.category_id chemical _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail rm ; absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration ; ad ; absolute configuration established by anomalous-dispersion effects in diffraction measurements on the crystal ; rmad ; absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration and confirmed by anomalous-dispersion effects in diffraction measurements on the crystal ; syn ; absolute configuration has not been established by anomalous-dispersion effects in diffraction measurements on the crystal. The enantiomer has been assigned by reference to an unchanging chiral centre in the synthetic procedure ; unk ; absolute configuration is unknown, there being no firm chemical evidence for its assignment to hand and it having not been established by anomalous-dispersion effects in diffraction measurements on the crystal. An arbitrary choice of enantiomer has been made ; . 'inapplicable' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_absolute_configuration' cif_core.dic 2.3 save_ save__chemical.melting_point_gt _item_description.description ; A temperature in kelvins above which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. _chemical.melting_point should always be used in preference to these two items whenever possible. ; _item.name '_chemical.melting_point_gt' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_related.related_name '_chemical.melting_point' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_melting_point_gt' cif_core.dic 2.3 save_ save__chemical.melting_point_lt _item_description.description ; A temperature in kelvins below which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. _chemical.melting_point should always be used in preference to these two items whenever possible. ; _item.name '_chemical.melting_point_lt' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_related.related_name '_chemical.melting_point' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_melting_point_lt' cif_core.dic 2.3 save_ save__chemical.optical_rotation _item_description.description ; The optical rotation in solution of the compound is specified in the following format: '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.\a/(l.c), where \a is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC as defined above, and SOLV is the chemical formula of the solvent. ; _item.name '_chemical.optical_rotation' _item.category_id chemical _item.mandatory_code no _item_type.code line _item_examples.case '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_optical_rotation' cif_core.dic 2.3 save_ save__chemical.properties_biological _item_description.description ; A free-text description of the biological properties of the material. ; _item.name '_chemical.properties_biological' _item.category_id chemical _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; diverse biological activities including use as a laxative and strong antibacterial activity against S. aureus and weak activity against cyclooxygenase-1 (COX-1) ; ; antibiotic activity against Bacillus subtilis (ATCC 6051) but no significant activity against Candida albicans (ATCC 14053), Aspergillus flavus (NRRL 6541) and Fusarium verticillioides (NRRL 25457) ; ; weakly potent lipoxygenase nonredox inhibitor ; ; no influenza A virus sialidase inhibitory and plaque reduction activities ; ; low toxicity against Drosophila melanogaster ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_properties_biological' cif_core.dic 2.3 save_ save__chemical.properties_physical _item_description.description ; A free-text description of the physical properties of the material. ; _item.name '_chemical.properties_physical' _item.category_id chemical _item.mandatory_code no _item_type.code text loop_ _item_examples.case air-sensitive moisture-sensitive hygroscopic deliquescent oxygen-sensitive photo-sensitive pyrophoric semiconductor 'ferromagnetic at low temperature' 'paramagnetic and thermochromic' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_properties_physical' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition _item_description.description ; The temperature in kelvins at which the solid decomposes. ; _item.name '_chemical.temperature_decomposition' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_examples.case 350 _item_related.related_name '_chemical.temperature_decomposition_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_decomposition' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition_esd _item_description.description ; The estimated standard deviation of _chemical.temperature_decomposition. ; _item.name '_chemical.temperature_decomposition_esd' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_related.related_name '_chemical.temperature_decomposition' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_chemical_temperature_decomposition_esd' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition_gt _item_description.description ; A temperature in kelvins above which the solid is known to decompose. _chemical.temperature_decomposition_gt and _chemical.temperature_decomposition_lt allow a range of temperatures to be given. _chemical.temperature_decomposition should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_decomposition_gt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_decomposition' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_decomposition_gt' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition_lt _item_description.description ; A temperature in kelvins below which the solid is known to decompose. _chemical.temperature_decomposition_gt and _chemical.temperature_decomposition_lt allow a range of temperatures to be given. _chemical.temperature_decomposition should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_decomposition_lt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_decomposition' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_decomposition_lt' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation _item_description.description ; The temperature in kelvins at which the solid sublimes. ; _item.name '_chemical.temperature_sublimation' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_examples.case 350 _item_related.related_name '_chemical.temperature_sublimation_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_sublimation' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation_esd _item_description.description ; The estimated standard deviation of _chemical.temperature_sublimation. ; _item.name '_chemical.temperature_sublimation_esd' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_related.related_name '_chemical.temperature_sublimation' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_chemical_temperature_sublimation_esd' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation_gt _item_description.description ; A temperature in kelvins above which the solid is known to sublime. _chemical.temperature_sublimation_gt and _chemical.temperature_sublimation_lt allow a range of temperatures to be given. _chemical.temperature_sublimation should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_sublimation_gt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_sublimation' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_sublimation_gt' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation_lt _item_description.description ; A temperature in kelvins below which the solid is known to sublime. _chemical.temperature_sublimation_gt and _chemical.temperature_sublimation_lt allow a range of temperatures to be given. _chemical.temperature_sublimation should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_sublimation_lt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_sublimation' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_sublimation_lt' cif_core.dic 2.3 save_ # save__citation.database_id_CSD _item_description.description ; Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure. ; _item.name '_citation.database_id_CSD' _item.category_id citation _item.mandatory_code no _item_type.code code _item_examples.case LEKKUH loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_citation_database_id_CSD' cif_core.dic 2.3 save_ save__database.CSD_history _item_description.description ; A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD). ; _item.name '_database.CSD_history' _item.category_id database _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_CSD_history' cif_core.dic 2.3 save_ save__database.code_CAS _item_description.description ; The code assigned by Chemical Abstracts. ; _item.name '_database.code_CAS' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_CAS' cif_core.dic 2.3 save_ save__database.code_CSD _item_description.description ; The code assigned by the Cambridge Structural Database. ; _item.name '_database.code_CSD' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_CSD' cif_core.dic 2.3 save_ save__database.code_ICSD _item_description.description ; The code assigned by the Inorganic Crystal Structure Database. ; _item.name '_database.code_ICSD' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_ICSD' cif_core.dic 2.3 save_ save__database.code_MDF _item_description.description ; The code assigned by the Metals Data File. ; _item.name '_database.code_MDF' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_MDF' cif_core.dic 2.3 save_ save__database.code_NBS _item_description.description ; The code assigned by the NBS (NIST) Crystal Data Database. ; _item.name '_database.code_NBS' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_NBS' cif_core.dic 2.3 save_ save__database.code_PDB _item_description.description ; The code assigned by the Protein Data Bank. ; _item.name '_database.code_PDB' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_PDB' cif_core.dic 2.3 save_ save__database.code_PDF _item_description.description ; The code assigned by the Powder Diffraction File (JCPDS/ICDD). ; _item.name '_database.code_PDF' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_PDF' cif_core.dic 2.3 save_ save__database.code_depnum_ccdc_fiz _item_description.description ; Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). ; _item.name '_database.code_depnum_ccdc_fiz' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_depnum_ccdc_fiz' cif_core.dic 2.3 save_ save__database.code_depnum_ccdc_journal _item_description.description ; Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). ; _item.name '_database.code_depnum_ccdc_journal' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_depnum_ccdc_journal' cif_core.dic 2.3 save_ save__database.code_depnum_ccdc_archive _item_description.description ; Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC. ; _item.name '_database.code_depnum_ccdc_archive' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_depnum_ccdc_archive' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure _item_description.description ; The mean hydrostatic pressure in kilopascals at which the intensities were measured. ; _item.name '_diffrn.ambient_pressure' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'kilopascals' _item_related.related_name '_diffrn.ambient_pressure_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_pressure' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure_esd _item_description.description ; The estimated standard deviation of _diffrn.ambient_pressure. ; _item.name '_diffrn.ambient_pressure_esd' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_units.code 'kilopascals' _item_related.related_name '_diffrn.ambient_pressure' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_diffrn_ambient_pressure' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure_gt _item_description.description ; The mean hydrostatic pressure in kilopascals above which the intensities were measured. _diffrn.ambient_pressure_gt and _diffrn.ambient_pressure_lt allow a pressure range to be given. _diffrn.ambient_pressure should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_pressure_gt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_pressure' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'kilopascals' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_pressure_gt' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure_lt _item_description.description ; The mean hydrostatic pressure in kilopascals below which the intensities were measured. _diffrn.ambient_pressure_gt and _diffrn.ambient_pressure_lt allow a pressure range to be given. _diffrn.ambient_pressure should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_pressure_lt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_pressure' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'kilopascals' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_pressure_lt' cif_core.dic 2.3 save_ # save__diffrn.ambient_temperature # _item_description.description # ; The mean temperature in kelvins at which the intensities # were measured. # ; # _item.name '_diffrn.ambient_temperature' # _item.category_id diffrn # _item.mandatory_code no # _item_type.code float # _item_type_conditions.code esd # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # _item_units.code kelvins # _item_related.related_name '_diffrn.ambient_temperature_esd' # _item_related.function_code associated_esd # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_diffrn_ambient_temperature' cif_core.dic 2.3 # save_ #save__diffrn.ambient_temperature_esd # _item_description.description #; The estimated standard deviation of _diffrn.ambient_temp. #; # _item.name '_diffrn.ambient_temperature_esd' # _item.category_id diffrn # _item.mandatory_code no # _item_type.code float # _item_units.code kelvins # _item_related.related_name '_diffrn.ambient_temp' # _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_diffrn_ambient_temperature_esd' cif_core.dic 2.3 # save_ save__diffrn.ambient_temp_gt _item_description.description ; The mean temperature in kelvins above which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. _diffrn.ambient_temp should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_temp_gt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_temp' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_temperature_gt' cif_core.dic 2.3 save_ save__diffrn.ambient_temp_lt _item_description.description ; The mean temperature in kelvins below which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. _diffrn.ambient_temp should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_temp_lt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_temp' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_temperature_lt' cif_core.dic 2.3 save_ save__diffrn_attenuator.material _item_description.description ; Material from which the attenuator is made. ; _item.name '_diffrn_attenuator.material' _item.category_id diffrn_attenuator _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_attenuator_material' cif_core.dic 2.3 save_ save__diffrn_detector.area_resol_mean _item_description.description ; The resolution of an area detector, in pixels/mm. ; _item.name '_diffrn_detector.area_resol_mean' _item.category_id diffrn_detector _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'pixels_per_millimetre' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_detector_area_resol_mean' cif_core.dic 2.3 save_ save__diffrn_detector.dtime _item_description.description ; The deadtime in microseconds of the detector used to measure the diffraction intensities. ; _item.name '_diffrn_detector.dtime' _item.category_id diffrn_detector _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . # _item_related.related_name '_diffrn_radiation_detector.dtime' # _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_detector_dtime' cif_core.dic 2.3 save_ save__diffrn_refln.class_code _item_description.description ; The code identifying the class to which this reflection has been assigned. This code must match a value of _diffrn_reflns_class.code. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. ; _item.name '_diffrn_refln.class_code' _item.category_id diffrn_refln _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_refln_class_code' cif_core.dic 2.3 save_ save__diffrn_refln.intensity_u _item_description.description ; Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_u' _item.category_id diffrn_refln _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_refln.intensity_sigma' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_refln_intensity_u' cif_core.dic 2.3 save_ save__diffrn_reflns.av_unetI/netI _item_description.description ; Measure [sum u(net I)|/sum|net I|] for all measured reflections. ; _item.name '_diffrn_reflns.av_unetI/netI' _item.category_id diffrn_reflns _item.mandatory_code no _item_type.code float # _item_related.related_name '_diffrn_reflns.av_sigmaI/netI' # _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_av_unetI/netI' cif_core.dic 2.3 save_ ######################### ## DIFFRN_REFLNS_CLASS ## ######################### save_diffrn_reflns_class _category.description ; Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment. ; _category.id 'diffrn_reflns_class' _category.mandatory_code no _category_key.name '_diffrn_reflns_class.code' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_reflns_class.number _diffrn_reflns_class.d_res_high _diffrn_reflns_class.d_res_low _diffrn_reflns_class.av_R_eq _diffrn_reflns_class.code _diffrn_reflns_class.description 1580 0.551 6.136 0.015 'Main' 'm=0; main reflections' 1045 0.551 6.136 0.010 'Sat1' 'm=1; first-order satellites' ; ; Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. Each reflection class is defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_reflns_class.av_R_eq _item_description.description ; For each reflection class, the residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The av|del(I)| term is the average absolute difference between av(I) and the individual intensities. ; _item.name '_diffrn_reflns_class.av_R_eq' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_av_R_eq' cif_core.dic 2.3 save_ save__diffrn_reflns_class.av_sgI/I _item_description.description ; Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities in a reflection class. ; _item.name '_diffrn_reflns_class.av_sgI/I' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_reflns_class.av_uI/I' _item_related.function_code replaces loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_av_sgI/I' cif_core.dic 2.3 save_ save__diffrn_reflns_class.av_uI/I _item_description.description ; Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class. ; _item.name '_diffrn_reflns_class.av_uI/I' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_reflns_class.av_sgI/I' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_av_uI/I' cif_core.dic 2.3 save_ save__diffrn_reflns_class.code _item_description.description ; The code identifying a certain reflection class. ; _item.name '_diffrn_reflns_class.code' _item.category_id diffrn_reflns_class _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' 'm1' 's2' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_code' cif_core.dic 2.3 save_ save__diffrn_reflns_class.description _item_description.description ; Description of each reflection class. ; _item.name '_diffrn_reflns_class.description' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'm=1 first order satellites' 'H0L0 common projection reflections' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_description' cif_core.dic 2.3 save_ save__diffrn_reflns_class.d_res_high _item_description.description ; The smallest value in angstroms for the interplanar spacings for the reflections in each measured reflection class. This is called the highest resolution for this reflection class. ; _item.name '_diffrn_reflns_class.d_res_high' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_d_res_high' cif_core.dic 2.3 save_ save__diffrn_reflns_class.d_res_low _item_description.description ; The largest value in angstroms of the interplanar spacings for the reflections for each measured reflection class. This is called the lowest resolution for this reflection class. ; _item.name '_diffrn_reflns_class.d_res_low' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_d_res_low' cif_core.dic 2.3 save_ save__diffrn_reflns_class.number _item_description.description ; The total number of measured intensities for each reflection class, excluding the systematic absences arising from centring translations. ; _item.name '_diffrn_reflns_class.number' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code int loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_number' cif_core.dic 2.3 save_ save__diffrn_source.take-off_angle _item_description.description ; The complement of the angle in degrees between the normal to the surface of the X-ray tube target and the primary X-ray beam for beams generated by traditional X-ray tubes. ; _item.name '_diffrn_source.take-off_angle' _item.category_id diffrn_source _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.00 0.00 0.00 90.0 90.0 90.0 _item_examples.case 1.5 _item_units.code 'degrees' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_source_take-off_angle' cif_core.dic 2.3 save_ save__diffrn_standards.scale_u _item_description.description ; The standard uncertainty of the individual mean standard scales applied to the intensity data. ; _item.name '_diffrn_standards.scale_u' _item.category_id diffrn_standards _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_standards.scale_sigma' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_standards_scale_u' cif_core.dic 2.3 save_ save__exptl_crystal.colour_lustre _item_description.description ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'. ; _item.name '_exptl_crystal.colour_lustre' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value metallic dull clear _item_related.related_name '_exptl_crystal.colour' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_colour_lustre' cif_core.dic 2.3 save_ save__exptl_crystal.colour_modifier _item_description.description ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'. ; _item.name '_exptl_crystal.colour_modifier' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value light dark whitish blackish grayish brownish reddish pinkish orangish yellowish greenish bluish _item_related.related_name '_exptl_crystal.colour' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_colour_modifier' cif_core.dic 2.3 save_ save__exptl_crystal.colour_primary _item_description.description ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'. ; _item.name '_exptl_crystal.colour_primary' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value colourless white black gray brown red pink orange yellow green blue violet _item_related.related_name '_exptl_crystal.colour' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_colour_primary' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas _item_description.description ; Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). ; _item.name '_exptl_crystal.density_meas' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_esd _item_description.description ; The estimated standard deviation of _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_meas_esd' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_exptl_crystal_density_meas_esd' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_gt _item_description.description ; The value above which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which _exptl_crystal.density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_meas_gt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 2.5 ; lower limit for the density (only the range within which the density lies was given in the original paper) ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_gt' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_lt _item_description.description ; The value below which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which _exptl_crystal.density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_meas_lt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 1.0 'specimen floats in water' 5.0 ; upper limit for the density (only the range within which the density lies was given in the original paper) ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_lt' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp _item_description.description ; Temperature in kelvins at which _exptl_crystal.density_meas was determined. ; _item.name '_exptl_crystal.density_meas_temp' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_temp' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp_esd _item_description.description ; The estimated standard deviation of _exptl_crystal.density_meas_temp. ; _item.name '_exptl_crystal.density_meas_temp_esd' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_units.code kelvins # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_exptl_crystal_density_meas_temp_esd' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp_gt _item_description.description ; Temperature in kelvins above which _exptl_crystal.density_meas was determined. _exptl_crystal.density_meas_temp_gt and _exptl_crystal.density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal.density_meas_temp. ; _item.name '_exptl_crystal.density_meas_temp_gt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_exptl_crystal.density_meas_temp' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_temp_gt' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp_lt _item_description.description ; Temperature in kelvins below which _exptl_crystal.density_meas was determined. _exptl_crystal.density_meas_temp_gt and _exptl_crystal.density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal.density_meas_temp. ; _item.name '_exptl_crystal.density_meas_temp_lt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_exptl_crystal.density_meas_temp' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 300 ; The density was measured at some unspecified temperature below room temperature. ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_temp_lt' cif_core.dic 2.3 save_ save__geom_bond.valence _item_description.description ; The bond valence calculated from _geom_bond.dist. ; _item.name '_geom_bond.valence' _item.category_id geom_bond _item.mandatory_code no _item_type.code int loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_geom_bond_valence' cif_core.dic 2.3 save_ save__publ_author.id_iucr _item_description.description ; Identifier in the IUCr contact database of a publication author. This identifier may be available from the World Directory of Crystallographers (http://wdc.iucr.org). ; _item.name '_publ_author.id_iucr' _item.category_id publ_author _item.mandatory_code no _item_type.code code _item_examples.case 2985 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_publ_author_id_iucr' cif_core.dic 2.3 save_ save__refine.ls_R_factor_gt _item_description.description ; Residual factor for the reflections (with number given by _reflns.number_gt) judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. This is the conventional R factor. See also _refine.ls_wR_factor_ definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_gt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_R_factor_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_R_factor_gt' cif_core.dic 2.3 save_ save__refine.ls_goodness_of_fit_gt _item_description.description ; The least-squares goodness-of-fit parameter S for significantly intense reflections (see _reflns.threshold_expression) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine.ls_restrained_S_ definitions. { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_gt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_goodness_of_fit_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_goodness_of_fit_gt' cif_core.dic 2.3 save_ save__refine.ls_goodness_of_fit_ref _item_description.description ; The least-squares goodness-of-fit parameter S for all reflections included in the refinement after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_ref' _item.category_id refine _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_goodness_of_fit_ref' cif_core.dic 2.3 save_ # save__refine.ls_shift/esd_max # _item_description.description # ; The largest ratio of the final least-squares parameter # shift to the final standard uncertainty (s.u., # formerly described as estimated standard deviation, e.s.d.). # ; # _item.name '_refine.ls_shift/esd_max' # _item.category_id refine # _item.mandatory_code no # _item_type.code float # _item_related.related_name '_refine.ls_shift/su_max' # _item_related.function_code replaces # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refine_ls_shift/esd_max' cif_core.dic 2.3 # save_ # # save__refine.ls_shift/esd_mean # _item_description.description # ; The average ratio of the final least-squares parameter # shift to the final standard uncertainty (s.u., # formerly described as estimated standard deviation, e.s.d.). # ; # # _item.name '_refine.ls_shift/esd_mean' # _item.category_id refine # _item.mandatory_code no # _item_type.code float # _item_related.related_name '_refine.ls_shift/su_mean' # _item_related.function_code replaces # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refine_ls_shift/esd_mean' cif_core.dic 2.3 # save_ save__refine.ls_shift_over_su_max _item_description.description ; The largest ratio of the final least-squares parameter shift to the final standard uncertainty. ; _item.name '_refine.ls_shift_over_su_max' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_esd_max' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_max' cif_core.dic 2.3 save_ save__refine.ls_shift_over_su_max_lt _item_description.description ; An upper limit for the largest ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the largest value of the shift divided by the final standard uncertainty is too small to measure. ; _item.name '_refine.ls_shift_over_su_max_lt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_su_max' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_max_lt' cif_core.dic 2.3 save_ save__refine.ls_shift_over_su_mean _item_description.description ; The average ratio of the final least-squares parameter shift to the final standard uncertainty. ; _item.name '_refine.ls_shift_over_su_mean' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_esd_mean' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_mean' cif_core.dic 2.3 save_ save__refine.ls_shift_over_su_mean_lt _item_description.description ; An upper limit for the average ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the average value of the shift divided by the final standard uncertainty is too small to measure. ; _item.name '_refine.ls_shift_over_su_mean_lt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_su_mean' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_mean_lt' cif_core.dic 2.3 save_ ##################### ## REFINE_LS_CLASS ## ##################### save_refine_ls_class _category.description ; Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately. ; _category.id 'refine_ls_class' _category.mandatory_code no _category_key.name '_refine_ls_class.code' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _refine_ls_class.R_factor_gt _refine_ls_class.code 0.057 'Main' 0.074 'Com' 0.064 'NbRefls' 0.046 'LaRefls' 0.112 'Sat1' 0.177 'Sat2' ; ; Example 1 - data for a modulated structure from van Smaalen [J. Phys. Condens. Matter (1991), 3, 1247-1263]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_class.code _item_description.description ; The code identifying a certain reflection class. This code must match a _reflns_class.code. ; _item.name '_refine_ls_class.code' _item.category_id refine_ls_class _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' 'm1' 's2' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_code' cif_core.dic 2.3 save_ save__refine_ls_class.d_res_high _item_description.description ; For each reflection class, the lowest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. ; _item.name '_refine_ls_class.d_res_high' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_d_res_high' cif_core.dic 2.3 save_ save__refine_ls_class.d_res_low _item_description.description ; For each reflection class, the highest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. ; _item.name '_refine_ls_class.d_res_low' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_d_res_low' cif_core.dic 2.3 save_ save__refine_ls_class.R_factor_gt _item_description.description ; For each reflection class, the residual factor for significantly intense reflections (see _reflns.threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of _refine_ls_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_factor_gt' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_factor_gt' cif_core.dic 2.3 save_ save__refine_ls_class.R_factor_all _item_description.description ; For each reflection class, the residual factor for all reflections satisfying the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of _refine_ls_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_factor_all' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_factor_all' cif_core.dic 2.3 save_ save__refine_ls_class.R_Fsqd_factor _item_description.description ; For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors, for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_Fsqd_factor' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_Fsqd_factor' cif_core.dic 2.3 save_ save__refine_ls_class.R_I_factor _item_description.description ; For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~ sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_I_factor' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_I_factor' cif_core.dic 2.3 save_ save__refine_ls_class.wR_factor_all _item_description.description ; For each reflection class, the weighted residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. See also the _refine_ls_class.R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine.ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.wR_factor_all' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_wR_factor_all' cif_core.dic 2.3 save_ save__refln.class_code _item_description.description ; The code identifying the class to which this reflection has been assigned. This code must match a value of _reflns_class.code. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. ; _item.name '_refln.class_code' _item.category_id refln _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_class_code' cif_core.dic 2.3 save_ save__refln.d_spacing _item_description.description ; The d spacing in angstroms for this reflection. This is related to the (sin theta)/lambda value by the expression _refln.d_spacing = 2/(_refln.sint/lambda). ; _item.name '_refln.d_spacing' _item.category_id refln _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_d_spacing' cif_core.dic 2.3 save_ save__refln.include_status _item_description.description ; Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. ; _item.name '_refln.include_status' _item.category_id refln _item.mandatory_code no _item_type.code code _item_related.related_name '_refln.status' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail o ; (lower-case letter o for 'observed') satisfies _refine.ls_d_res_high satisfies _refine.ls_d_res_low exceeds _reflns.threshold_expression ; < ; satisfies _refine.ls_d_res_high satisfies _refine.ls_d_res_low does not exceed _reflns.threshold_expression ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine.ls_d_res_high' l 'does not satisfy _refine.ls_d_res_low' # _item_default.value o loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_include_status' cif_core.dic 2.3 save_ save__refln.mean_path_length_tbar _item_description.description ; Mean path length in millimetres through the crystal for this reflection. ; _item.name '_refln.mean_path_length_tbar' _item.category_id refln _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'millimetres' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_mean_path_length_tbar' cif_core.dic 2.3 save_ # save__refln.observed_status # _item_description.description # ; Classification of a reflection so as to indicate its status # with respect to inclusion in refinement and calculation of # R factors. # ; # # _item.name '_refln.observed_status' # _item.category_id refln # _item.mandatory_code no # _item_type.code code # _item_related.related_name '_refln.include_status' # _item_related.function_code replaces # loop_ # _item_enumeration.value # _item_enumeration.detail # o # ; satisfies _refine.ls_d_res_high # satisfies _refine.ls_d_res_low # observed by _reflns_observed_criterion # ; # < # ; satisfies _refine.ls_d_res_high # satisfies _refine.ls_d_res_low # unobserved by _reflns.observed_criterion # ; # - 'systematically absent reflection' # x 'unreliable measurement -- not used' # h 'does not satisfy _refine.ls_d_res_high' # l 'does not satisfy _refine.ls_d_res_low' # # # _item_default.value o # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refln_observed_status' cif_core.dic 2.3 # save_ # save__refln.sint/lambda # _item_description.description # ; The (sin theta)/lambda value in reciprocal angstroms for this # reflection. # ; # _item.name '_refln.sint/lambda' # _item.category_id refln # _item.mandatory_code no # _item_type.code float # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # _item_units.code 'reciprocal_angstroms' # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refln_sint/lambda' cif_core.dic 2.3 # save_ save__reflns.Friedel_coverage _item_description.description ; The proportion of Friedel-related reflections present in the number of 'independent' reflections specified by the item _reflns.number_all. This proportion is calculated as the ratio: [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the DIFFRN_REFLN list, N(Crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. Examples: (a) For centrosymmetric structures, the value of _reflns.Friedel_coverage is necessarily equal to 0.0, as the crystal class is identical to the Laue symmetry. (b) For whole-sphere data for a crystal in the space group P1, _reflns.Friedel_coverage is equal to 1.0, as no reflection h k l is equivalent to -h -k -l in the crystal class and all Friedel pairs {h k l; -h -k -l} have been measured. (c) For whole-sphere data in space group Pmm2, _reflns.Friedel_coverage will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are nonzero, they are when l=0. (d) For a crystal in space group Pmm2, measurements of the two inequivalent octants h >= 0, k >=0, l lead to the same value as in (c), whereas measurements of the two equivalent octants h >= 0, k, l >= 0 will lead to a zero value for _reflns.Friedel_coverage. ; _item.name '_reflns.Friedel_coverage' _item.category_id reflns _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_Friedel_coverage' cif_core.dic 2.3 save_ save__reflns.number_gt _item_description.description ; The number of reflections in the REFLN list (not the DIFFRN_REFLN list) that are significantly intense, satisfying the criterion specified by _reflns.threshold_expression. This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details. ; _item.name '_reflns.number_gt' _item.category_id reflns _item.mandatory_code no _item_type.code int # _item_related.related_name '_reflns.number_observed' # _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_number_gt' cif_core.dic 2.3 save_ save__reflns.threshold_expression _item_description.description ; The threshold, usually based on multiples of u(I), u(F^2^) or u(F), that serves to identify significantly intense reflections, the number of which is given by _reflns.number_gt. These reflections are used in the calculation of _refine.ls_R_factor_gt. ; _item.name '_reflns.threshold_expression' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_threshold_expression' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.3 loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate _item_type.code text _item_examples.case 'I>2u(I)' save_ ################## ## REFLNS_CLASS ## ################## save_reflns_class _category.description ; Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class. ; _category.id 'reflns_class' _category.mandatory_code no _category_key.name '_reflns_class.code' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _reflns_class.number_gt _reflns_class.code 584 'Main' 226 'Sat1' 50 'Sat2' ; ; Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns_class.code _item_description.description ; The code identifying a certain reflection class. ; _item.name '_reflns_class.code' _item.category_id reflns_class _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' 'm1' 's2' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_code' cif_core.dic 2.3 save_ save__reflns_class.description _item_description.description ; Description of each reflection class. ; _item.name '_reflns_class.description' _item.category_id reflns_class _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'm=1 first order satellites' 'H0L0 common projection reflections' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_description' cif_core.dic 2.3 save_ save__reflns_class.d_res_high _item_description.description ; For each reflection class, the smallest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. ; _item.name '_reflns_class.d_res_high' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_d_res_high' cif_core.dic 2.3 save_ save__reflns_class.d_res_low _item_description.description ; For each reflection class, the largest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. ; _item.name '_reflns_class.d_res_low' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_d_res_low' cif_core.dic 2.3 save_ save__reflns_class.number_gt _item_description.description ; For each reflection class, the number of significantly intense reflections (see _reflns.threshold_expression) in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel- equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details. ; _item.name '_reflns_class.number_gt' _item.category_id reflns_class _item.mandatory_code no _item_type.code int loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_number_gt' cif_core.dic 2.3 save_ save__reflns_class.number_total _item_description.description ; For each reflection class, the total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details. ; _item.name '_reflns_class.number_total' _item.category_id reflns_class _item.mandatory_code no _item_type.code int loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_number_total' cif_core.dic 2.3 save_ save__reflns_class.R_factor_all _item_description.description ; For each reflection class, the residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of _reflns_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_factor_all' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_factor_all' cif_core.dic 2.3 save_ save__reflns_class.R_factor_gt _item_description.description ; For each reflection class, the residual factor for significantly intense reflections (see _reflns.threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of _reflns_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_factor_gt' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_factor_gt' cif_core.dic 2.3 save_ save__reflns_class.R_Fsqd_factor _item_description.description ; For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_Fsqd_factor' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_Fsqd_factor' cif_core.dic 2.3 save_ save__reflns_class.R_I_factor _item_description.description ; For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_I_factor' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_I_factor' cif_core.dic 2.3 save_ save__reflns_class.wR_factor_all _item_description.description ; For each reflection class, the weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. See also _reflns_class.R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine.ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.wR_factor_all' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_wR_factor_all' cif_core.dic 2.3 save_ save__reflns_shell.meanI_over_sigI_gt _item_description.description ; The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. ; _item.name '_reflns_shell.meanI_over_sigI_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.meanI_over_uI_gt' _item_related.function_code replaces loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_meanI_over_sigI_gt' cif_core.dic 2.3 save_ save__reflns_shell.meanI_over_uI_all _item_description.description ; The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. ; _item.name '_reflns_shell.meanI_over_uI_all' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.meanI_over_sigI_all' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_meanI_over_uI_all' cif_core.dic 2.3 save_ save__reflns_shell.meanI_over_uI_gt _item_description.description ; The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. ; _item.name '_reflns_shell.meanI_over_uI_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_reflns_shell.meanI_over_sigI_gt' alternate '_reflns_shell.meanI_over_sigI_obs' alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_meanI_over_uI_gt' cif_core.dic 2.3 save_ save__reflns_shell.number_measured_gt _item_description.description ; The number of significantly intense reflections (see _reflns.threshold_expression) measured for this shell. ; _item.name '_reflns_shell.number_measured_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code int _item_related.related_name '_reflns_shell.number_measured_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_number_measured_gt' cif_core.dic 2.3 save_ save__reflns_shell.number_unique_gt _item_description.description ; The total number of significantly intense reflections (see _reflns.threshold_expression) resulting from merging measured symmetry-equivalent reflections for this resolution shell. ; _item.name '_reflns_shell.number_unique_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code int _item_related.related_name '_reflns_shell.number_unique_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_number_unique_gt' cif_core.dic 2.3 save_ save__reflns_shell.percent_possible_gt _item_description.description ; The percentage of geometrically possible reflections represented by significantly intense reflections (see _reflns.threshold_expression) measured for this shell. ; _item.name '_reflns_shell.percent_possible_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.percent_possible_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_percent_possible_gt' cif_core.dic 2.3 save_ save__reflns_shell.Rmerge_F_gt _item_description.description ; The value of Rmerge(F) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sum~i~ ( sum~j~ | F~j~ - | ) Rmerge(F) = -------------------------------- sum~i~ ( sum~j~ ) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. ; _item.name '_reflns_shell.Rmerge_F_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.Rmerge_F_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_Rmerge_F_gt' cif_core.dic 2.3 save_ save__reflns_shell.Rmerge_I_gt _item_description.description ; The value of Rmerge(I) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sum~i~ ( sum~j~ | I~j~ - | ) Rmerge(I) = -------------------------------- sum~i~ ( sum~j~ ) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. ; _item.name '_reflns_shell.Rmerge_I_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.Rmerge_I_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_Rmerge_I_gt' cif_core.dic 2.3 save_ ################# ## SPACE_GROUP ## ################# save_space_group _category.description ; Contains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in this dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary. ; _category.id 'space_group' _category.mandatory_code no _category_key.name '_space_group.id' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _space_group.id 1 _space_group.name_H-M_alt 'C 2/c' _space_group.IT_number 15 _space_group.name_Hall '-C 2yc' _space_group.crystal_system monoclinic ; ; Example 1 - the monoclinic space group No. 15 with unique axis b. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__space_group.crystal_system _item_description.description ; The name of the system of geometric crystal classes of space groups (crystal system) to which the space group belongs. Note that rhombohedral space groups belong to the trigonal system. ; _item.name '_space_group.crystal_system' _item.category_id space_group _item.mandatory_code no _item_type.code code _item_related.related_name '_symmetry.cell_setting' _item_related.function_code alternate loop_ _item_enumeration.value triclinic monoclinic orthorhombic tetragonal trigonal hexagonal cubic loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_crystal_system' cif_core.dic 2.3 save_ save__space_group.id _item_description.description ; This is the unique identifier for the SPACE_GROUP category. ; _item.name '_space_group.id' _item.category_id space_group _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_id' cif_core.dic 2.3 save_ save__space_group.IT_number _item_description.description ; The number as assigned in International Tables for Crystallography Vol. A, specifying the proper affine class (i.e. the orientation-preserving affine class) of space groups (crystallographic space-group type) to which the space group belongs. This number defines the space-group type but not the coordinate system in which it is expressed. ; _item.name '_space_group.IT_number' _item.category_id space_group _item.mandatory_code no _item_type.code int _item_related.related_name '_symmetry.Int_Tables_number' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 1 1 1 230 230 230 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_IT_number' cif_core.dic 2.3 save_ save__space_group.name_Hall _item_description.description ; Space-group symbol defined by Hall. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. _space_group.name_Hall uniquely defines the space group and its reference to a particular coordinate system. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. [See also International Tables for Crystallography Vol. B (2001), Chapter 1.4, Appendix 1.4.2.] ; _item.name '_space_group.name_Hall' _item.category_id space_group _item.mandatory_code no _item_type.code line _item_related.related_name '_symmetry.space_group_name_Hall' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 'P 2c -2ac' 'equivalent to Pca21' '-I 4bd 2ab 3' 'equivalent to Ia3d' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_name_Hall' cif_core.dic 2.3 save_ save__space_group.name_H-M_alt _item_description.description ; _space_group.name_H-M_alt allows any Hermann-Mauguin symbol to be given. The way in which this item is used is determined by the user and in general is not intended to be interpreted by computer. It may, for example, be used to give one of the extended Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. Subscripts should appear without special symbols. Bars should be given as negative signs before the numbers to which they apply. The commonly used Hermann-Mauguin symbol determines the space- group type uniquely but a given space-group type may be described by more than one Hermann-Mauguin symbol. The space- group type is best described using _space_group.IT_number. The Hermann-Mauguin symbol may contain information on the choice of basis, but not on the choice of origin. To define the setting uniquely, use _space_group.name_Hall or list the symmetry operations. ; _item.name '_space_group.name_H-M_alt' _item.category_id space_group _item.mandatory_code no _item_type.code line _item_related.related_name '_symmetry.space_group_name_H-M' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail ; loop_ _space_group.name_H-M_alt 'C m c m' 'C 2/c 2/m 21/m' 'A m a m' ; 'three examples for space group No. 63' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_name_H-M_alt' cif_core.dic 2.3 save_ ####################### ## SPACE_GROUP_SYMOP ## ####################### save_space_group_symop _category.description ; Contains information about the symmetry operations of the space group. ; _category.id 'space_group_symop' _category.mandatory_code no _category_key.name '_space_group_symop.id' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,-y,-z 3 -x,1/2+y,1/2-z 4 x,1/2-y,1/2+z ; ; Example 1 - The symmetry operations for the space group P21/c. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__space_group_symop.id _item_description.description ; An arbitrary identifier that uniquely labels each symmetry operation in the list. ; _item.name '_space_group_symop.id' _item.category_id space_group_symop _item.mandatory_code yes _item_type.code code _item_related.related_name '_symmetry_equiv.id' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_symop_id' cif_core.dic 2.3 save_ save__space_group_symop.operation_xyz _item_description.description ; A parsable string giving one of the symmetry operations of the space group in algebraic form. If W is a matrix representation of the rotational part of the symmetry operation defined by the positions and signs of x, y and z, and w is a column of translations defined by the fractions, an equivalent position X' is generated from a given position X by the equation X' = WX + w (Note: X is used to represent bold_italics_x in International Tables for Crystallography Vol. A, Part 5) When a list of symmetry operations is given, it must contain a complete set of coordinate representatives which generates all the operations of the space group by the addition of all primitive translations of the space group. Such representatives are to be found as the coordinates of the general-equivalent position in International Tables for Crystallography Vol. A (2002), to which it is necessary to add any centring translations shown above the general-equivalent position. That is to say, it is necessary to list explicity all the symmetry operations required to generate all the atoms in the unit cell defined by the setting used. ; _item.name '_space_group_symop.operation_xyz' _item.category_id space_group_symop _item.mandatory_code no _item_type.code line # _item_default.value 'x,y,z' _item_related.related_name '_symmetry_equiv.pos_as_xyz' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 'x,1/2-y,1/2+z' ; glide reflection through the plane (x,1/4,z), with glide vector 1/2 c ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_symop_operation_xyz' cif_core.dic 2.3 save_ save__space_group_symop.sg_id _item_description.description ; This must match a particular value of _space_group.id, allowing the symmetry operation to be identified with a particular space group. ; _item.name '_space_group_symop.sg_id' _item.category_id space_group_symop _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_symop_sg_id' cif_core.dic 2.3 save_ ################### ## VALENCE_PARAM ## ################### save_valence_param _category.description ; Data items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths. In addition to the parameters, a pointer is given to the reference (in VALENCE_REF) from which the bond-valence parameters were taken. ; _category.id 'valence_param' _category.mandatory_code no loop_ _category_key.name '_valence_param.atom_1' '_valence_param.atom_1_valence' '_valence_param.atom_2' '_valence_param.atom_2_valence' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _valence_param.atom_1 _valence_param.atom_1_valence _valence_param.atom_2 _valence_param.atom_2_valence _valence_param.Ro _valence_param.B _valence_param.ref_id _valence_param.details Cu 2 O -2 1.679 0.37 a . Cu 2 O -2 1.649 0.37 j . Cu 2 N -3 1.64 0.37 m '2-coordinate N' Cu 2 N -3 1.76 0.37 m '3-coordinate N' loop_ _valence_ref.id _valence_ref.reference a 'Brown & Altermatt (1985), Acta Cryst. B41, 244-247' j 'Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205' m 'See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375' ; ; Example 1 - a bond-valence parameter list with accompanying references. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__valence_param.atom_1 _item_description.description ; The element symbol of the first atom forming the bond whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_1' _item.category_id valence_param _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_1' cif_core.dic 2.3 save_ save__valence_param.atom_1_valence _item_description.description ; The valence (formal charge) of the first atom whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_1_valence' _item.category_id valence_param _item.mandatory_code yes _item_type.code int loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_1_valence' cif_core.dic 2.3 save_ save__valence_param.atom_2 _item_description.description ; The element symbol of the second atom forming the bond whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_2' _item.category_id valence_param _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_2' cif_core.dic 2.3 save_ save__valence_param.atom_2_valence _item_description.description ; The valence (formal charge) of the second atom whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_2_valence' _item.category_id valence_param _item.mandatory_code yes _item_type.code int loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_2_valence' cif_core.dic 2.3 save_ save__valence_param.B _item_description.description ; The bond-valence parameter B used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. ; _item.name '_valence_param.B' _item.category_id valence_param _item.mandatory_code no _item_type.code float _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_B' cif_core.dic 2.3 save_ save__valence_param.details _item_description.description ; Details of or comments on the bond-valence parameters. ; _item.name '_valence_param.details' _item.category_id valence_param _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_details' cif_core.dic 2.3 save_ save__valence_param.id _item_description.description ; An identifier for the valence parameters of a bond between the given atoms. ; _item.name '_valence_param.id' _item.category_id valence_param _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_id' cif_core.dic 2.3 save_ save__valence_param.ref_id _item_description.description ; An identifier which links to the reference to the source from which the bond-valence parameters are taken. A child of _valence_ref.id which it must match. ; _item.name '_valence_param.ref_id' _item.category_id valence_param _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_ref_id' cif_core.dic 2.3 save_ save__valence_param.Ro _item_description.description ; The bond-valence parameter Ro used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. ; _item.name '_valence_param.Ro' _item.category_id valence_param _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_Ro' cif_core.dic 2.3 save_ ################# ## VALENCE_REF ## ################# save_valence_ref _category.description ; Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken. ; _category.id 'valence_ref' _category.mandatory_code no _category_key.name '_valence_ref.id' save_ save__valence_ref.id _item_description.description ; An identifier for items in this category. Parent of _valence_param.ref_id, which must have the same value. ; _item.name '_valence_ref.id' _item.category_id valence_ref _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_ref_id' cif_core.dic 2.3 save_ save__valence_ref.reference _item_description.description ; Literature reference from which the valence parameters identified by _valence_param.id were taken. ; _item.name '_valence_ref.reference' _item.category_id valence_ref _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_ref_reference' cif_core.dic 2.3 save_ #-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof ########################################################################### # # File: mmcif_pdbx-def-2.dic # # PDB Exchange Data Dictionary # # This data dictionary contains definitions used by wwPDB for data exchange # and data processing. # # Definition Section 2 # # ########################################################################### save_pdbx_audit _category.description ; The PDBX_AUDIT holds current version information. ; _category.id 'pdbx_audit' _category.mandatory_code no loop_ _category_key.name '_pdbx_audit.entry_id' loop_ _category_group.id 'inclusive_group' 'audit_group' save_ save__pdbx_audit.entry_id _item_description.description ; The value of _pdbx_audit.entry_id identifies the data block. ; _item.name '_pdbx_audit.entry_id' _item.category_id pdbx_audit _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_audit.entry_id' _item_linked.parent_name '_entry.id' _item_examples.case 'BDL001' save_ save__pdbx_audit.current_version _item_description.description ; The value of _pdbx_audit.entry_id identifies the data block. ; _item.name '_pdbx_audit.current_version' _item.category_id pdbx_audit _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_audit.current_version' _item_linked.parent_name '_audit.revision_id' _item_examples.case '1' save_ ### ### ####################### ## PDBX_AUDIT_AUTHOR ## ####################### save_pdbx_audit_author _category.description ; Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block. ; _category.id pdbx_audit_author _category.mandatory_code no _category_key.name '_pdbx_audit_author.ordinal' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _pdbx_audit_author.name _pdbx_audit_author.address _pdbx_audit_author.ordinal 'Fitzgerald, Paula M.D.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 1 'McKeever, Brian M.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 2 'Van Middlesworth, J.F.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 3 'Springer, James P.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 4 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_audit_author.address _item_description.description ; The address of an author of this data block. If there are multiple authors, _pdbx_audit_author.address is looped with _pdbx_audit_author.name. ; _item.name '_pdbx_audit_author.address' _item.category_id pdbx_audit_author _item.mandatory_code no _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__pdbx_audit_author.name _item_description.description ; The name of an author of this data block. If there are multiple authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address. The family name(s), followed by a comma and including any dynastic compoents, precedes the first name(s) or initial(s). ; _item.name '_pdbx_audit_author.name' _item.category_id pdbx_audit_author _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__pdbx_audit_author.ordinal _item_description.description ; A unique sequential integer identifier for each author. ; _item.name '_pdbx_audit_author.ordinal' _item.category_id pdbx_audit_author _item.mandatory_code yes _item_type.code int loop_ _item_examples.case 1 2 3 save_ ### ### save_pdbx_database_message _category.description ; The PDBX_DATABASE_MESSAGE category provides information about correspondance related to a structure deposition. ; _category.id 'pdbx_database_message' _category.mandatory_code no loop_ _category_key.name '_pdbx_database_message.message_id' '_pdbx_database_message.entry_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdbx_group' save_ save__pdbx_database_message.entry_id _item_description.description ; The value of _pdbx_database_message.entry_id identifies the data block. ; _item.name '_pdbx_database_message.entry_id' _item.category_id pdbx_database_message _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_database_message.entry_id' _item_linked.parent_name '_entry.id' _item_examples.case 'BDL001' _item_aliases.alias_name '_ndb_database_message.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.message_id _item_description.description ; This is an unique and sequential identifier for a message. ; _item.name '_pdbx_database_message.message_id' _item.category_id pdbx_database_message _item.mandatory_code yes _item_type.code text _item_examples.case 'message 1' _item_aliases.alias_name '_ndb_database_message.message_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.date _item_description.description ; This is the date when a message was sent or received. ; _item.name '_pdbx_database_message.date' _item.category_id pdbx_database_message _item.mandatory_code yes _item_type.code yyyy-mm-dd:hh:mm _item_aliases.alias_name '_ndb_database_message.date' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.content_type _item_description.description ; This code defines the content of the message. ; _item.name '_pdbx_database_message.content_type' _item.category_id pdbx_database_message _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail DEPOSIT 'A component of a deposition or revision' REMINDER 'A message reminding the depositor to send materials' QUERY 'A query to a depositor for specific information' OTHER 'A miscellaneous message' _item_aliases.alias_name '_ndb_database_message.content_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.message_type _item_description.description ; Defines how the message was sent or received. ; _item.name '_pdbx_database_message.message_type' _item.category_id pdbx_database_message _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail FAX 'A facsimile message' EMAIL 'An electronic mail message' MAIL 'A conventional mail message' PHONE 'A phone message' _item_aliases.alias_name '_ndb_database_message.message_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.sender _item_description.description ; The name of the sender. ; _item.name '_pdbx_database_message.sender' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_ndb_database_message.sender' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.sender_address_fax _item_description.description ; The FAX phone number of the sender. ; _item.name '_pdbx_database_message.sender_address_fax' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code fax _item_aliases.alias_name '_ndb_database_message.sender_address_fax' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.sender_address_phone _item_description.description ; The phone number of the sender. ; _item.name '_pdbx_database_message.sender_address_phone' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code phone _item_aliases.alias_name '_ndb_database_message.sender_address_phone' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.sender_address_email _item_description.description ; The email address of the sender. ; _item.name '_pdbx_database_message.sender_address_email' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code email _item_aliases.alias_name '_ndb_database_message.sender_address_email' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.sender_address_mail _item_description.description ; The postal address of the sender. ; _item.name '_pdbx_database_message.sender_address_mail' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_ndb_database_message.sender_address_mail' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.receiver _item_description.description ; The name of the receiver. ; _item.name '_pdbx_database_message.receiver' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_ndb_database_message.receiver' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.receiver_address_fax _item_description.description ; The FAX phone number of the receiver. ; _item.name '_pdbx_database_message.receiver_address_fax' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code fax _item_aliases.alias_name '_ndb_database_message.receiver_address_fax' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.receiver_address_phone _item_description.description ; The phone number of the receiver. ; _item.name '_pdbx_database_message.receiver_address_phone' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code phone _item_aliases.alias_name '_ndb_database_message.receiver_address_phone' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.receiver_address_email _item_description.description ; The email address of the receiver. ; _item.name '_pdbx_database_message.receiver_address_email' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code email _item_aliases.alias_name '_ndb_database_message.receiver_address_email' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.receiver_address_mail _item_description.description ; The postal address of the receiver. ; _item.name '_pdbx_database_message.receiver_address_mail' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_ndb_database_message.receiver_address_mail' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_message.message _item_description.description ; The text of the message. ; _item.name '_pdbx_database_message.message' _item.category_id pdbx_database_message _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_ndb_database_message.message' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### save_pdbx_database_PDB_obs_spr _category.description ; The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders for information on obsolete/superseded PDB entries ; _category.id 'pdbx_database_PDB_obs_spr' _category.mandatory_code no loop_ _category_key.name '_pdbx_database_PDB_obs_spr.pdb_id' '_pdbx_database_PDB_obs_spr.replace_pdb_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdbx_group' save_ save__pdbx_database_PDB_obs_spr.id _item_description.description ; Identifier for the type of obsolete entry to be added to this entry. ; _item.name '_pdbx_database_PDB_obs_spr.id' _item.category_id pdbx_database_PDB_obs_spr _item.mandatory_code yes _item_type.code code _item_examples.case 'OBSLTE' loop_ _item_enumeration.value 'OBSLTE' 'SPRSDE' _item_aliases.alias_name '_ndb_database_PDB_obs_spr.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_PDB_obs_spr.date _item_description.description ; The date of replacement. ; _item.name '_pdbx_database_PDB_obs_spr.date' _item.category_id pdbx_database_PDB_obs_spr _item.mandatory_code yes _item_type.code yyyy-mm-dd:hh:mm _item_examples.case '1997-03-30' _item_aliases.alias_name '_ndb_database_PDB_obs_spr.date' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_PDB_obs_spr.pdb_id _item_description.description ; The new PDB identifier for the replaced entry. ; _item.name '_pdbx_database_PDB_obs_spr.pdb_id' _item.category_id pdbx_database_PDB_obs_spr _item.mandatory_code yes _item_type.code code _item_examples.case 2ABC _item_aliases.alias_name '_ndb_database_PDB_obs_spr.pdb_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_PDB_obs_spr.replace_pdb_id _item_description.description ; The PDB identifier for the replaced (OLD) entry. ; _item.name '_pdbx_database_PDB_obs_spr.replace_pdb_id' _item.category_id pdbx_database_PDB_obs_spr _item.mandatory_code yes _item_type.code code _item_examples.case 3ABC _item_aliases.alias_name '_ndb_database_PDB_obs_spr.replace_pdb_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ### save_pdbx_database_proc _category.description ; Internal records to track the data processing cycle. ; _category.id 'pdbx_database_proc' _category.mandatory_code no loop_ _category_key.name '_pdbx_database_proc.cycle_id' '_pdbx_database_proc.entry_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdbx_group' _category_examples.case ; _pdbx_database_proc.entry_id 'BDL001' _pdbx_database_proc.cycle_id 1 _pdbx_database_proc.date_begin_cycle 1998-02-27 _pdbx_database_proc.date_end_cycle 1998-02-27 ; save_ save__pdbx_database_proc.entry_id _item_description.description ; The value of _pdbx_database_proc.entry_id identifies the data block. ; _item.name '_pdbx_database_proc.entry_id' _item.category_id pdbx_database_proc _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_database_proc.entry_id' _item_linked.parent_name '_entry.id' _item_examples.case 'BDL001' _item_aliases.alias_name '_ndb_database_proc.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_proc.cycle_id _item_description.description ; This is a number of the processing cycle. ; _item.name '_pdbx_database_proc.cycle_id' _item.category_id pdbx_database_proc _item.mandatory_code yes _item_type.code code _item_examples.case '1 for the initial cycle' _item_aliases.alias_name '_ndb_database_proc.cycle_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_proc.date_begin_cycle _item_description.description ; This is the date of the start of the processing cycle. ; _item.name '_pdbx_database_proc.date_begin_cycle' _item.category_id pdbx_database_proc _item.mandatory_code yes _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-27 _item_aliases.alias_name '_ndb_database_proc.date_begin_cycle' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_proc.date_end_cycle _item_description.description ; This is the date of the end of the processing cycle. ; _item.name '_pdbx_database_proc.date_end_cycle' _item.category_id pdbx_database_proc _item.mandatory_code yes _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-27 _item_aliases.alias_name '_ndb_database_proc.date_end_cycle' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_proc.details _item_description.description ; Special details about the current processing cycle. ; _item.name '_pdbx_database_proc.details' _item.category_id pdbx_database_proc _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_ndb_database_proc.details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ### save_pdbx_database_remark _category.description ; Data items in the PDBX_DATABASE_REMARK category record keep additional information about the entry. They are mostly used to create 'non-standard' PDB REMARK annotations (6-99). ; _category.id pdbx_database_remark _category.mandatory_code no _category_key.name '_pdbx_database_remark.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 1ABC ; ; loop_ _pdbx_database_remark.id _pdbx_database_remark.text 1 ; THE NON-CRYSTALLOGRAPHIC RELATIONSHIP BETWEEN THE THREE DOUBLE HELICES IN THE ASYMMETRIC UNIT IS DESCRIBED IN THE MTRIX1-3 RECORDS. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_database_remark.id _item_description.description ; A unique identifier for the PDB remark record. ; _item.name '_pdbx_database_remark.id' _item.category_id pdbx_database_remark _item.mandatory_code yes _item_type.code int _item_aliases.alias_name '_rcsb_database_PDB_remark.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_remark.text _item_description.description ; The full text of the PDB remark record. ; _item.name '_pdbx_database_remark.text' _item.category_id pdbx_database_remark _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_rcsb_database_PDB_remark.text' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### save_pdbx_database_status _category.description ; These are internal RCSB records to keep track of data processing and status of the entry. ; _category.id 'pdbx_database_status' _category.mandatory_code no _category_key.name '_pdbx_database_status.entry_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdbx_group' _category_examples.case ; _pdbx_database_status.entry_id 1ABC _pdbx_database_status.status_code REL _pdbx_database_status.author_release_status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 1996-02-13 _pdbx_database_status.date_author_approval 1996-02-13 _pdbx_database_status.recvd_author_approval Y _pdbx_database_status.author_approval_type EXPLICIT _pdbx_database_status.hold_for_publication N _pdbx_database_status.date_hold_coordinates 1996-02-13 _pdbx_database_status.date_hold_struct_fact 1996-02-13 _pdbx_database_status.date_of_PDB_release 1996-02-14 _pdbx_database_status.date_deposition_form 1996-02-13 _pdbx_database_status.date_coordinates 1996-02-13 _pdbx_database_status.date_struct_fact 1996-02-13 _pdbx_database_status.date_manuscript 1996-02-13 _pdbx_database_status.date_nmr_constraints ? _pdbx_database_status.recvd_deposit_form Y _pdbx_database_status.recvd_coordinates Y _pdbx_database_status.recvd_struct_fact Y _pdbx_database_status.recvd_manuscript Y _pdbx_database_status.recvd_nmr_constraints N ; save_ save__pdbx_database_status.status_code _item_description.description ; Code for status of file. ; _item.name '_pdbx_database_status.status_code' _item.category_id pdbx_database_status _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail PROC 'Processing in progress' WAIT 'Awaiting author approval' REL 'Released' HOLD 'On hold until yyyy-mm-dd' HPUB 'On hold until publication' OBS 'Entry has been obsoleted and replaced by another entry' DEL 'Entry has been deleted' WDRN 'Entry has been withdrawn' BIB 'Only a bibliographic entry exists for this entry; there are no coordinates' REV 'Entry currently under revision' UPD 'Deprecated code' loop_ _item_examples.case REL HOLD REV BIB _item_aliases.alias_name '_ndb_database_status.status_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.author_release_status_code _item_description.description ; The release status authorized by the depositor. ; _item.name '_pdbx_database_status.author_release_status_code' _item.category_id pdbx_database_status _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail REL 'Release' HOLD 'On hold until yyyy-mm-dd' HPUB 'On hold until publication' OBS 'Entry has been obsoleted and replaced by another entry' WDRN 'Entry has been withdrawn' _item_examples.case ; REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor ; _item_aliases.alias_name '_ndb_database_status.author_release_status_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.status_code_sf _item_description.description ; Code for status of structure factor file. ; _item.name '_pdbx_database_status.status_code_sf' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail PROC 'Processing in progress' REL 'Release' HOLD 'On hold until yyyy-mm-dd' HPUB 'On hold until publication' OBS 'Entry has been obsoleted and replaced by another entry' WDRN 'Entry has been withdrawn' WAIT 'Awaiting author approval' _item_examples.case ; PROC = Processing in progress REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor WAIT = Awaiting author approval ; _item_aliases.alias_name '_ndb_database_status.status_code_sf' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.status_code_mr _item_description.description ; Code for status of NMR constraints file. ; _item.name '_pdbx_database_status.status_code_mr' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail PROC 'Processing in progress' REL 'Release' HOLD 'On hold until yyyy-mm-dd' HPUB 'On hold until publication' OBS 'Entry has been obsoleted and replaced by another entry' WDRN 'Entry has been withdrawn' WAIT 'Awaiting author approval' _item_examples.case ; PROC = Processing in progress REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor WAIT = Awaiting author approval ; _item_aliases.alias_name '_ndb_database_status.status_code_mr' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.dep_release_code_coordinates _item_description.description ; The deposited coordinates for this deposition will be released according the value of this item. ; _item.name '_pdbx_database_status.dep_release_code_coordinates' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code line _item_default.value 'RELEASE NOW' loop_ _item_enumeration.value _item_enumeration.detail 'RELEASE NOW' 'Release immediately' 'HOLD FOR PUBLICATION' 'Hold until primary citation is published' 'HOLD FOR 6 WEEKS' 'Hold for 6 weeks' 'HOLD FOR 6 MONTHS' 'Hold for 6 months' 'HOLD FOR 1 YEAR' 'Hold for 1 year' _item_examples.case ; RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year ; _item_aliases.alias_name '_ndb_database_status.dep_release_code_coordinates' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.dep_release_code_sequence _item_description.description ; The sequence information for this deposition will be released according the value of this item. Setting this status code to "RELEASE NOW" indicates that the macromolecular sequence(s) for this entry may be displayed in PDB status reports prior to the release of the entry. Setting this status code to "HOLD FOR RELEASE" conceals the sequence information in PDB status reports until the coordinate data for this entry are released. ; _item.name '_pdbx_database_status.dep_release_code_sequence' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code line # _item_default.value 'RELEASE NOW' loop_ _item_enumeration.value _item_enumeration.detail 'RELEASE NOW' 'Release sequence information in status reports immediately' 'HOLD FOR RELEASE' ;Conceal sequence information in status reports until coordinate data is released ; _item_examples.case ; RELEASE NOW = Release sequence information in status reports immediately HOLD FOR RELEASE = Conceal sequence information in status reports until coordinate data is release ; _item_aliases.alias_name '_ndb_database_status.dep_release_code_sequence' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.dep_release_code_struct_fact _item_description.description ; The deposited structure factors for this deposition will be released according the value of this item. ; _item.name '_pdbx_database_status.dep_release_code_struct_fact' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code line _item_default.value 'RELEASE NOW' # loop_ # _item_enumeration.value # _item_enumeration.detail # 'RELEASE NOW' 'Release immediately' # 'HOLD FOR PUBLICATION' 'Hold until primary citation is published' # 'HOLD FOR 6 MONTHS' 'Hold for 6 months' # 'HOLD FOR 1 YEAR' 'Hold for 1 year' # 'HOLD FOR 4 YEARS' 'Hold for 4 years' _item_examples.case ; RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year ; _item_aliases.alias_name '_ndb_database_status.dep_release_code_struct_fact' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.dep_release_code_nmr_constraints _item_description.description ; The deposited NMR constrait data for this deposition will be released according the value of this item. ; _item.name '_pdbx_database_status.dep_release_code_nmr_constraints' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code line _item_default.value 'RELEASE NOW' # loop_ # _item_enumeration.value # _item_enumeration.detail # 'RELEASE NOW' 'Release immediately' # 'HOLD FOR PUBLICATION' 'Hold until primary citation is published' # 'HOLD FOR 6 MONTHS' 'Hold for 6 months' # 'HOLD FOR 1 YEAR' 'Hold for 1 year' _item_examples.case ; RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year ; _item_aliases.alias_name '_ndb_database_status.dep_release_code_nmr_constraints' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.entry_id _item_description.description ; The value of _pdbx_database_status.entry_id identifies the data block. ; _item.name '_pdbx_database_status.entry_id' _item.category_id pdbx_database_status _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_database_status.entry_id' _item_linked.parent_name '_entry.id' _item_examples.case 'BDL001' _item_aliases.alias_name '_ndb_database_status.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_deposit_form _item_description.description ; This code indicates whether the deposition form for an entry has been received. ; _item.name '_pdbx_database_status.recvd_deposit_form' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.recvd_deposit_form' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_deposition_form _item_description.description ; The date the deposition form is received. ; _item.name '_pdbx_database_status.date_deposition_form' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1982-02-21 _item_aliases.alias_name '_ndb_database_status.date_deposition_form' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_coordinates _item_description.description ; This code indicates whether the coordinates for an entry have been received. ; _item.name '_pdbx_database_status.recvd_coordinates' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.recvd_coordinates' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_coordinates _item_description.description ; The date the coordinates are received. ; _item.name '_pdbx_database_status.date_coordinates' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-21 _item_aliases.alias_name '_ndb_database_status.date_coordinates' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_struct_fact _item_description.description ; This code indicates whether the structure factors for an entry have been received. ; _item.name '_pdbx_database_status.recvd_struct_fact' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.recvd_struct_fact' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_struct_fact _item_description.description ; The date the structure factors are received. ; _item.name '_pdbx_database_status.date_struct_fact' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-28 _item_aliases.alias_name '_ndb_database_status.date_struct_fact' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ # save__pdbx_database_status.recvd_nmr_constraints _item_description.description ; This code indicates whether the NMR contraint data for an entry have been received. ; _item.name '_pdbx_database_status.recvd_nmr_constraints' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.recvd_nmr_constraints' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_nmr_constraints _item_description.description ; The date the structure factors are received. ; _item.name '_pdbx_database_status.date_nmr_constraints' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-28 _item_aliases.alias_name '_ndb_database_status.date_nmr_constraints' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_internal_approval _item_description.description ; This code indicates whether the internal approval for an entry have been received. ; _item.name '_pdbx_database_status.recvd_internal_approval' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.recvd_internal_approval' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_manuscript _item_description.description ; This code indicates whether the manuscript for an entry has been received. ; _item.name '_pdbx_database_status.recvd_manuscript' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.recvd_manuscript' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_manuscript _item_description.description ; The date the manuscript is received. ; _item.name '_pdbx_database_status.date_manuscript' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-28 _item_aliases.alias_name '_ndb_database_status.date_manuscript' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.name_depositor _item_description.description ; The last name of the depositor to be used in correspondance. ; _item.name '_pdbx_database_status.name_depositor' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code text _item_examples.case 'Smith' _item_aliases.alias_name '_ndb_database_status.name_depositor' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_author_approval _item_description.description ; This code indicates whether the author's approval for an entry has been received. ; _item.name '_pdbx_database_status.recvd_author_approval' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.recvd_author_approval' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.author_approval_type _item_description.description ; This code indicates whether the author's approval for an entry was received explicitly or implicitly. The latter is automatically implied by failure to respond to the validation summary within the prescribed period. ; _item.name '_pdbx_database_status.author_approval_type' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value implicit explicit _item_examples.case ; implicit = automatic approval by failure to acknowledge explicit = approval via depositor acknowledgement ; _item_aliases.alias_name '_ndb_database_status.author_approval_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_author_approval _item_description.description ; The date the author's approval is received. ; _item.name '_pdbx_database_status.date_author_approval' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-20 _item_aliases.alias_name '_ndb_database_status.date_author_approval' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_initial_deposition_date _item_description.description ; The date of initial deposition. (The first message for deposition has been received.) ; _item.name '_pdbx_database_status.recvd_initial_deposition_date' _item.category_id pdbx_database_status _item.mandatory_code yes _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-21 _item_aliases.alias_name '_ndb_database_status.recvd_initial_deposition_date' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_submitted _item_description.description ; The date of complete deposition. This corresponds to the date at which the PDB identifier is assigned. ; _item.name '_pdbx_database_status.date_submitted' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-20 _item_aliases.alias_name '_ndb_database_status.date_submitted' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.rcsb_annotator _item_description.description ; The initials of the annotator processing this entry. ; _item.name '_pdbx_database_status.rcsb_annotator' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'BS' 'SJ' 'KB' _item_aliases.alias_name '_ndb_database_status.rcsb_annotator' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_of_sf_release _item_description.description ; The date of PDB/RCSB release. This corresponds to the date at which the entry is placed into the public archive. ; _item.name '_pdbx_database_status.date_of_sf_release' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case 1999-02-28 _item_aliases.alias_name '_ndb_database_status.date_of_sf_release' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_of_mr_release _item_description.description ; The date of PDB/RCSB release. This corresponds to the date at which the entry is placed into the public archive. ; _item.name '_pdbx_database_status.date_of_mr_release' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case 1999-02-28 _item_aliases.alias_name '_ndb_database_status.date_of_mr_release' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_of_PDB_release _item_description.description ; PDB release date. This is the date that appears in the PDB REVDAT record. ; _item.name '_pdbx_database_status.date_of_PDB_release' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-28 _item_aliases.alias_name '_ndb_database_status.date_of_PDB_release' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_hold_coordinates _item_description.description ; At an author's request, a coordinate entry may be held after processing for some period of time. ; _item.name '_pdbx_database_status.date_hold_coordinates' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-28 _item_aliases.alias_name '_ndb_database_status.date_hold_coordinates' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_hold_struct_fact _item_description.description ; At an author's request, the structure factors may be held after processing for some period of time. ; _item.name '_pdbx_database_status.date_hold_struct_fact' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-28 _item_aliases.alias_name '_ndb_database_status.date_hold_struct_fact' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.date_hold_nmr_constraints _item_description.description ; At an author's request, the NMR constraint data may be held after processing for some period of time. ; _item.name '_pdbx_database_status.date_hold_nmr_constraints' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-28 _item_aliases.alias_name '_ndb_database_status.date_hold_nmr_constraints' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.hold_for_publication _item_description.description ; At an author's request, an entry is to be held until publication. ; _item.name '_pdbx_database_status.hold_for_publication' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.hold_for_publication' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.SG_entry _item_description.description ; This code indicates whether the entry belongs to Structural Genomics Project. ; _item.name '_pdbx_database_status.SG_entry' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code uchar1 loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_examples.case Y _item_aliases.alias_name '_ndb_database_status.SG_entry' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.pdb_date_of_author_approval _item_description.description ; This is the date when PDB received the author's approval for an entry which has been processed by NDB. (This is a place holder for entries processed before Jan. 1, 1996.) ; _item.name '_pdbx_database_status.pdb_date_of_author_approval' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case 1983-02-27 _item_aliases.alias_name '_ndb_database_status.pdb_date_of_author_approval' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.deposit_site _item_description.description ; The site where the file was deposited. ; _item.name '_pdbx_database_status.deposit_site' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code code loop_ _item_examples.case NDB RCSB PDB EBI OSAKA BNL loop_ _item_enumeration.value NDB RCSB PDB EBI OSAKA BNL _item_aliases.alias_name '_ndb_database_status.deposit_site' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.process_site _item_description.description ; The site where the file was deposited. ; _item.name '_pdbx_database_status.process_site' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code code loop_ _item_examples.case NDB RCSB EBI OSAKA PDB PRAGUE loop_ _item_enumeration.value NDB RCSB EBI OSAKA PDB PRAGUE _item_aliases.alias_name '_ndb_database_status.process_site' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### save_pdbx_entity_name _category.description ; The PDBX_ENTITY_NAME records additional name information for each entity. ; _category.id pdbx_entity_name _category.mandatory_code no loop_ _category_key.name '_pdbx_entity_name.entity_id' '_pdbx_entity_name.name' '_pdbx_entity_name.name_type' loop_ _category_group.id 'inclusive_group' 'entity_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _pdbx_entity_name.entity_id _pdbx_entity_name.name _pdbx_entity_name.name_type 1 "PLASTOCYANIN" 'SWS-NAME' 1 "Electron transport" 'SWS-KEYWORD' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_entity_name.entity_id _item_description.description ; Pointer to _entity.id. ; _item.name '_pdbx_entity_name.entity_id' _item.category_id pdbx_entity_name _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_entity_name.entity_id' _item_linked.parent_name '_entity.id' _item_aliases.alias_name '_rcsb_entity_name.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_name.name _item_description.description ; Entity name. ; _item.name '_pdbx_entity_name.name' _item.category_id pdbx_entity_name _item.mandatory_code yes _item_type.code line _item_aliases.alias_name '_rcsb_entity_name.name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_name.name_type _item_description.description ; Entity name type. ; _item.name '_pdbx_entity_name.name_type' _item.category_id pdbx_entity_name _item.mandatory_code yes _item_type.code line _item_aliases.alias_name '_rcsb_entity_name.name_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 loop_ _item_enumeration.value 'RCSB_NAME' 'RCSB_SYNONYM' 'SWS-NAME' 'SWS-SYNONYM' 'SWS-KEYWORD' 'GB-NAME' 'GB-SYNONYM' 'GB-KEYWORD' save_ ### ### save_pdbx_prerelease_seq _category.description ; This category provides a placeholder for pre-release sequence information. After release this category should be discarded. ; _category.id pdbx_prerelease_seq _category.mandatory_code no _category_key.name '_pdbx_prerelease_seq.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' 'pdbx_group' loop_ _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _pdbx_prerelease_seq.entity_id _pdbx_prerelease_seq.seq_one_letter_code 1 'GKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD' 2 'HKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNN' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_prerelease_seq.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_pdbx_prerelease_seq.entity_id' _item.category_id pdbx_prerelease_seq _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_prerelease_seq.entity_id' _item_linked.parent_name '_entity.id' _item_aliases.alias_name '_rcsb_prerelease_seq.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_prerelease_seq.seq_one_letter_code _item_description.description ; Chemical sequence expressed as string of one-letter amino acid codes. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil ; _item.name '_pdbx_prerelease_seq.seq_one_letter_code' _item.category_id pdbx_prerelease_seq _item.mandatory_code no _item_type.code text _item_examples.case ; MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD ; _item_aliases.alias_name '_rcsb_prerelease_seq.seq_one_letter_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ### save_pdbx_poly_seq_scheme _category.description ; The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities. ; _category.id pdbx_poly_seq_scheme _category.mandatory_code no loop_ _category_key.name '_pdbx_poly_seq_scheme.asym_id' '_pdbx_poly_seq_scheme.entity_id' '_pdbx_poly_seq_scheme.seq_id' '_pdbx_poly_seq_scheme.mon_id' loop_ _category_group.id 'inclusive_group' 'struct_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB entry DDFB25 ; ; loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_num _pdbx_poly_seq_scheme.pdb_num _pdbx_poly_seq_scheme.auth_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 C 1 1 1 C C A . A 1 2 G 2 2 2 G G A . A 1 3 T 3 3 3 T T A . A 1 4 +A 4 4 4 +A +A A . A 1 5 C 5 5 5 C C A . A 1 6 G 6 6 6 G G A . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_poly_seq_scheme.asym_id _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_pdbx_poly_seq_scheme.asym_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_poly_seq_scheme.asym_id' _item_linked.parent_name '_struct_asym.id' loop_ _item_examples.case '1' 'A' '2B3' _item_aliases.alias_name '_ndb_poly_seq_scheme.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.entity_id _item_description.description ; Pointer to _entity.id. ; _item.name '_pdbx_poly_seq_scheme.entity_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_poly_seq_scheme.entity_id' _item_linked.parent_name '_entity.id' _item_aliases.alias_name '_ndb_poly_seq_scheme.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.seq_id _item_description.description ; Pointer to _entity_poly_seq.num ; _item.name '_pdbx_poly_seq_scheme.seq_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code code _item_linked.parent_name '_pdbx_poly_seq_scheme.seq_id' _item_linked.child_name '_entity_poly_seq.num' _item_aliases.alias_name '_ndb_poly_seq_scheme.seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.mon_id _item_description.description ; Pointer to _entity_poly_seq.mon_id. ; _item.name '_pdbx_poly_seq_scheme.mon_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_poly_seq_scheme.mon_id' _item_linked.parent_name '_entity_poly_seq.mon_id' _item_aliases.alias_name '_ndb_poly_seq_scheme.mon_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.pdb_strand_id _item_description.description ; PDB strand/chain id. ; _item.name '_pdbx_poly_seq_scheme.pdb_strand_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.ndb_seq_num _item_description.description ; NDB residue number. ; _item.name '_pdbx_poly_seq_scheme.ndb_seq_num' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.ndb_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.pdb_seq_num _item_description.description ; PDB residue number. ; _item.name '_pdbx_poly_seq_scheme.pdb_seq_num' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.auth_seq_num _item_description.description ; _atom_site.auth_seq_id ; _item.name '_pdbx_poly_seq_scheme.auth_seq_num' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.auth_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.pdb_mon_id _item_description.description ; PDB residue name. ; _item.name '_pdbx_poly_seq_scheme.pdb_mon_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_mon_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.auth_mon_id _item_description.description ; _atom_site.auth_comp_id ; _item.name '_pdbx_poly_seq_scheme.auth_mon_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.auth_mon_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.pdb_ins_code _item_description.description ; PDB insertion code. ; _item.name '_pdbx_poly_seq_scheme.pdb_ins_code' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save_pdbx_nonpoly_scheme _category.description ; The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities. ; _category.id pdbx_nonpoly_scheme _category.mandatory_code no loop_ _category_key.name '_pdbx_nonpoly_scheme.asym_id' '_pdbx_nonpoly_scheme.ndb_seq_num' loop_ _category_group.id 'inclusive_group' 'struct_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 HOH 100 100 100 HOH HOH C . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nonpoly_scheme.asym_id _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_pdbx_nonpoly_scheme.asym_id' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nonpoly_scheme.asym_id' _item_linked.parent_name '_atom_site.label_asym_id' loop_ _item_examples.case '1' 'A' '2B3' _item_aliases.alias_name '_ndb_nonpoly_scheme.asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.entity_id _item_description.description ; Pointer to _atom_site.label_entity_id. ; _item.name '_pdbx_nonpoly_scheme.entity_id' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_nonpoly_scheme.entity_id' _item_linked.parent_name '_atom_site.label_entity_id' _item_aliases.alias_name '_ndb_nonpoly_scheme.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.mon_id _item_description.description ; Pointer to _atom_site.label_comp_id. ; _item.name '_pdbx_nonpoly_scheme.mon_id' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_nonpoly_scheme.mon_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_ndb_nonpoly_scheme.mon_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.pdb_strand_id _item_description.description ; PDB strand/chain id. ; _item.name '_pdbx_nonpoly_scheme.pdb_strand_id' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.ndb_seq_num _item_description.description ; NDB/RCSB residue number. ; _item.name '_pdbx_nonpoly_scheme.ndb_seq_num' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_nonpoly_scheme.ndb_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.pdb_seq_num _item_description.description ; PDB residue number. ; _item.name '_pdbx_nonpoly_scheme.pdb_seq_num' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.auth_seq_num _item_description.description ; _atom_site.auth_seq_id ; _item.name '_pdbx_nonpoly_scheme.auth_seq_num' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_nonpoly_scheme.auth_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.pdb_mon_id _item_description.description ; PDB residue name. ; _item.name '_pdbx_nonpoly_scheme.pdb_mon_id' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_mon_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.auth_mon_id _item_description.description ; _atom_site.auth_comp_id ; _item.name '_pdbx_nonpoly_scheme.auth_mon_id' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_nonpoly_scheme.auth_mon_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nonpoly_scheme.pdb_ins_code _item_description.description ; PDB insertion code. ; _item.name '_pdbx_nonpoly_scheme.pdb_ins_code' _item.category_id pdbx_nonpoly_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ### save_pdbx_refine _category.description ; Data items in the PDBX_REFINE category record details about additional structure refinement parameters which are needed to complete legacy REMARK 3 refinement templates in PDB format files. ; _category.id pdbx_refine _category.mandatory_code no _category_key.name '_pdbx_refine.entry_id' loop_ _category_group.id 'inclusive_group' 'refine_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - PDB placeholders for refinement program SHELX ; ; _pdbx_refine.entry_id ABC001 _pdbx_refine.R_factor_all_4sig_cutoff 0.174 _pdbx_refine.R_factor_obs_4sig_cutoff 0.169 _pdbx_refine.number_reflns_obs_4sig_cutoff 1263 _pdbx_refine.free_R_factor_4sig_cutoff 0.216 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 164 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 1.29 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_refine.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_pdbx_refine.entry_id' _item.category_id pdbx_refine _item.mandatory_code yes _item_linked.child_name '_pdbx_refine.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_ndb_refine.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.R_factor_all_no_cutoff _item_description.description ; R-value (all reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.R_factor_all_no_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_ndb_refine.R_factor_all_no_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.R_factor_obs_no_cutoff _item_description.description ; R-value (working set reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.R_factor_obs_no_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_ndb_refine.R_factor_obs_no_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.free_R_factor_4sig_cutoff _item_description.description ; R free value (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.free_R_factor_4sig_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_examples.case 0.216 _item_aliases.alias_name '_ndb_refine.free_R_factor_4sig_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.free_R_factor_no_cutoff _item_description.description ; Free R-value (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.free_R_factor_no_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_ndb_refine.free_R_factor_no_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.free_R_val_test_set_size_perc_no_cutoff _item_description.description ; Free R-value test set size (in percent, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.free_R_val_test_set_size_perc_no_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_ndb_refine.free_R_val_test_set_size_perc_no_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.free_R_val_test_set_ct_no_cutoff _item_description.description ; Free R-value test set count (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.free_R_val_test_set_ct_no_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_ndb_refine.free_R_val_test_set_ct_no_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.number_reflns_obs_no_cutoff _item_description.description ; Total number of reflections (no cutoff). Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.number_reflns_obs_no_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_ndb_refine.number_reflns_obs_no_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.R_factor_all_4sig_cutoff _item_description.description ; R-value (all reflections, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.R_factor_all_4sig_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_examples.case 0.174 _item_aliases.alias_name '_ndb_refine.R_factor_all_4sig_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.R_factor_obs_4sig_cutoff _item_description.description ; R-value (working set, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.R_factor_obs_4sig_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_examples.case 0.169 _item_aliases.alias_name '_ndb_refine.R_factor_obs_4sig_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.free_R_val_4sig_cutoff _item_description.description ; Free R-value (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.free_R_val_4sig_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_ndb_refine.free_R_val_4sig_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff _item_description.description ; Free R-value test set size (in percent, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_examples.case 1.29 _item_aliases.alias_name '_ndb_refine.free_R_val_test_set_size_perc_4sig_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.free_R_val_test_set_ct_4sig_cutoff _item_description.description ; Free R-value test set count (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.free_R_val_test_set_ct_4sig_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_examples.case 164 _item_aliases.alias_name '_ndb_refine.free_R_val_test_set_ct_4sig_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine.number_reflns_obs_4sig_cutoff _item_description.description ; Total number of reflections (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. ; _item.name '_pdbx_refine.number_reflns_obs_4sig_cutoff' _item.category_id pdbx_refine _item.mandatory_code no _item_type.code float _item_examples.case 1263 _item_aliases.alias_name '_ndb_refine.number_reflns_obs_4sig_cutoff' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ############################# ## PDBX_STRUCT_SHEET_HBOND ## ############################# save_pdbx_struct_sheet_hbond _category.description ; Data items in the PDBX_STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta sheet. This category is provided for cases where only a single hydrogen bond is used to register the two residue ranges. Category STRUCT_SHEET_HBOND should be used when the initial and terminal hydrogen bonds for strand pair are known. ; _category.id pdbx_struct_sheet_hbond _category.mandatory_code no loop_ _category_key.name '_pdbx_struct_sheet_hbond.sheet_id' '_pdbx_struct_sheet_hbond.range_id_1' '_pdbx_struct_sheet_hbond.range_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' 'pdbx_group' save_ save__pdbx_struct_sheet_hbond.range_id_1 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_pdbx_struct_sheet_hbond.range_id_1' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_id_1' _item_linked.parent_name '_struct_sheet_range.id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_id_1' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_id_2 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_pdbx_struct_sheet_hbond.range_id_2' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_id_2' _item_linked.parent_name '_struct_sheet_range.id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_id_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_pdbx_struct_sheet_hbond.sheet_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.sheet_id' _item_linked.parent_name '_struct_sheet.id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.sheet_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__pdbx_struct_sheet_hbond.range_1_label_atom_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_label_atom_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code yes _item_type.code atcode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_atom_id' _item_linked.parent_name '_atom_site.label_atom_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_atom_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_label_seq_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_label_seq_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_label_comp_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_label_comp_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code ucode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_label_asym_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_label_asym_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_auth_atom_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_auth_atom_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code atcode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_atom_id' _item_linked.parent_name '_atom_site.auth_atom_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_atom_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_auth_seq_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_auth_seq_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_auth_comp_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_auth_comp_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code ucode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_auth_asym_id _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_auth_asym_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_1_PDB_ins_code _item_description.description ; A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_1_PDB_ins_code' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_PDB_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__pdbx_struct_sheet_hbond.range_2_label_atom_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_label_atom_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code yes _item_type.code atcode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_atom_id' _item_linked.parent_name '_atom_site.label_atom_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_atom_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_label_seq_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_label_seq_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_label_comp_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_label_comp_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code ucode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_label_asym_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_label_asym_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_auth_atom_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_auth_atom_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code atcode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_atom_id' _item_linked.parent_name '_atom_site.auth_atom_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_atom_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_auth_seq_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_auth_seq_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_auth_comp_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_auth_comp_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code ucode _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_auth_asym_id _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_auth_asym_id' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_struct_sheet_hbond.range_2_PDB_ins_code _item_description.description ; A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_struct_sheet_hbond.range_2_PDB_ins_code' _item.category_id pdbx_struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_PDB_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### save_pdbx_xplor_file _category.description ; Parameter and topology files used in X-PLOR/CNS refinement. ; _category.id pdbx_xplor_file _category.mandatory_code no _category_key.name '_pdbx_xplor_file.serial_no' loop_ _category_group.id 'inclusive_group' 'refine_group' 'pdbx_group' loop_ _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _pdbx_xplor_file.serial_no 1 _pdbx_xplor_file.param_file parm_hol.dat _pdbx_xplor_file.topol_file topol_hol.dat ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_xplor_file.serial_no _item_description.description ; Serial number. ; _item.name '_pdbx_xplor_file.serial_no' _item.category_id pdbx_xplor_file _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_ndb_xplor_file.serial_no' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_xplor_file.param_file _item_description.description ; Parameter file name in X-PLOR/CNS refinement. ; _item.name '_pdbx_xplor_file.param_file' _item.category_id pdbx_xplor_file _item.mandatory_code no _item_type.code line _item_examples.case 'PARAM_NDBX_HIGH.DNA' _item_aliases.alias_name '_ndb_xplor_file.param_file' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_xplor_file.topol_file _item_description.description ; Topology file name in X-PLOR/CNS refinement. ; _item.name '_pdbx_xplor_file.topol_file' _item.category_id pdbx_xplor_file _item.mandatory_code no _item_type.code line _item_examples.case 'TOP_NDBX.DNA' _item_aliases.alias_name '_ndb_xplor_file.topol_file' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save_pdbx_refine_aux_file _category.description ; Auxilary parameter and topology files used in refinement. ; _category.id pdbx_refine_aux_file _category.mandatory_code no _category_key.name '_pdbx_refine_aux_file.serial_no' loop_ _category_group.id 'inclusive_group' 'refine_group' 'pdbx_group' loop_ _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _pdbx_refine_aux_file.serial_no 1 _pdbx_refine_aux_file.file_name parm_hol.dat _pdbx_refine_aux_file.file_type PARAMETER ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_refine_aux_file.serial_no _item_description.description ; Serial number. ; _item.name '_pdbx_refine_aux_file.serial_no' _item.category_id pdbx_refine_aux_file _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_rcsb_refine_aux_file.serial_no' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine_aux_file.file_name _item_description.description ; Auxilary file name. ; _item.name '_pdbx_refine_aux_file.file_name' _item.category_id pdbx_refine_aux_file _item.mandatory_code no _item_type.code line _item_examples.case 'PARAM_NDBX_HIGH.DNA' _item_aliases.alias_name '_rcsb_refine_aux_file.file_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_refine_aux_file.file_type _item_description.description ; Auxilary file type. ; _item.name '_pdbx_refine_aux_file.file_type' _item.category_id pdbx_refine_aux_file _item.mandatory_code no _item_type.code line _item_examples.case 'PARAMETER' loop_ _item_enumeration.value 'PARAMETER' 'TOPOLOGY' _item_aliases.alias_name '_rcsb_refine_aux_file.file_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## ## save_pdbx_database_related _category.description ; Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry. ; _category.id pdbx_database_related _category.mandatory_code no loop_ _category_key.name '_pdbx_database_related.db_name' '_pdbx_database_related.db_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' _category_examples.case ; _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1ABC ; save_ save__pdbx_database_related.db_name _item_description.description ; The name of the database containing the related entry. ; _item.name '_pdbx_database_related.db_name' _item.category_id pdbx_database_related _item.mandatory_code yes _item_type.code code # loop_ # _item_enumeration.value 'PDB' 'NDB' 'BMRB' 'BMCD' _item_examples.case ; PDB - Protein Databank NDB - Nucleic Acid Database BMRB - BioMagResBank BMCD - Biological Macromolecule Crystallization Database ; _item_aliases.alias_name '_rcsb_database_related.db_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_related.details _item_description.description ; A description of the related entry. ; _item.name '_pdbx_database_related.details' _item.category_id pdbx_database_related _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; 1ABC contains the same protein complexed with Netropsin. ; _item_aliases.alias_name '_rcsb_database_related.details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ # # save__pdbx_database_related.db_id _item_description.description ; The identifying code in the related database. ; _item.name '_pdbx_database_related.db_id' _item.category_id pdbx_database_related _item.mandatory_code yes _item_type.code line loop_ _item_examples.case '1ABC' 'BDL001' _item_aliases.alias_name '_rcsb_database_related.db_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ # save__pdbx_database_related.content_type _item_description.description ; The identifying content type of the related entry. ; _item.name '_pdbx_database_related.content_type' _item.category_id pdbx_database_related _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'minimized average structure' 'representative structure' 'ensemble' 'derivative structure' 'native structure' 'other' loop_ _item_enumeration.value 'minimized average structure' 'representative structure' 'ensemble' 'derivative structure' 'native structure' 'other' _item_aliases.alias_name '_rcsb_database_related.content_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ########################## ## PDBX_ENTITY_ASSEMBLY ## ########################## save_pdbx_entity_assembly _category.description ; The PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities. ; _category.id pdbx_entity_assembly _category.mandatory_code no loop_ _category_key.name '_pdbx_entity_assembly.id' '_pdbx_entity_assembly.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; A complex composed of one copy of entities 1 and 2. ; ; loop_ _pdbx_entity_assembly.id _pdbx_entity_assembly.biol_id _pdbx_entity_assembly.entity_id _pdbx_entity_assembly.num_copies 1 1 1 1 1 1 2 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_entity_assembly.id _item_description.description ; An identifier for the assembly. ; _item.name '_pdbx_entity_assembly.id' _item.category_id pdbx_entity_assembly _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_rcsb_entity_assembly.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_assembly.entity_id _item_description.description ; An enity identifier. A reference to _entity.id. ; _item.name '_pdbx_entity_assembly.entity_id' _item.category_id pdbx_entity_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_entity_assembly.entity_id' _item_linked.parent_name '_entity.id' _item_aliases.alias_name '_rcsb_entity_assembly.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_assembly.biol_id _item_description.description ; An identifier for the assembly. ; _item.name '_pdbx_entity_assembly.biol_id' _item.category_id pdbx_entity_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_entity_assembly.biol_id' _item_linked.parent_name '_struct_biol.id' _item_aliases.alias_name '_rcsb_entity_assembly.biol_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_assembly.num_copies _item_description.description ; The number of copies of this entity in the assembly. ; _item.name '_pdbx_entity_assembly.num_copies' _item.category_id pdbx_entity_assembly _item.mandatory_code yes _item_type.code int _item_aliases.alias_name '_rcsb_entity_assembly.num_copies' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ######################### ## PDBX_ENTITY_SRC_SYN ## ######################### save_pdbx_entity_src_syn _category.description ; PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit. ; _category.id pdbx_entity_src_syn _category.mandatory_code no _category_key.name '_pdbx_entity_src_syn.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' 'pdbx_group' save_ save__pdbx_entity_src_syn.details _item_description.description ; A description of special aspects of the source for the synthetic entity. ; _item.name '_pdbx_entity_src_syn.details' _item.category_id pdbx_entity_src_syn _item.mandatory_code no _item_type.code text _item_examples.case 'This sequence occurs naturally in humans.' _item_aliases.alias_name '_rcsb_entity_src_syn.details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_src_syn.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_pdbx_entity_src_syn.entity_id' _item.category_id pdbx_entity_src_syn _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_entity_src_syn.entity_id' _item_linked.parent_name '_entity.id' loop_ _item_examples.case '1' '2' '3' '4' _item_aliases.alias_name '_rcsb_entity_src_syn.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### --------------------------------------------------------------------------- ### Supplemental items in existing mmCIF categories ... ### ### save__atom_site.pdbx_auth_alt_id _item_description.description ; Author's alternate location identifier. ; _item.name '_atom_site.pdbx_auth_alt_id' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_auth_alt_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.pdbx_PDB_ins_code _item_description.description ; PDB insertion code. ; _item.name '_atom_site.pdbx_PDB_ins_code' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.pdbx_PDB_model_num _item_description.description ; PDB model number. ; _item.name '_atom_site.pdbx_PDB_model_num' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_model' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.pdbx_PDB_residue_no _item_description.description ; PDB residue number. ; _item.name '_atom_site.pdbx_PDB_residue_no' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_PDB_residue_no' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.pdbx_PDB_residue_name _item_description.description ; PDB residue name. ; _item.name '_atom_site.pdbx_PDB_residue_name' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_PDB_residue_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.pdbx_PDB_strand_id _item_description.description ; PDB strand id. ; _item.name '_atom_site.pdbx_PDB_strand_id' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_PDB_strand_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.pdbx_PDB_atom_name _item_description.description ; PDB atom name. ; _item.name '_atom_site.pdbx_PDB_atom_name' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_PDB_atom_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.pdbx_auth_atom_name _item_description.description ; Author's atom name. ; _item.name '_atom_site.pdbx_auth_atom_name' _item.category_id atom_site _item.mandatory_code no _item_type.code atcode _item_aliases.alias_name '_atom_site.ndb_auth_atom_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__atom_site_anisotrop.pdbx_auth_seq_id _item_description.description ; Pointer to _atom_site.auth_seq_id ; _item.name '_atom_site_anisotrop.pdbx_auth_seq_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_residue_no' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_auth_alt_id _item_description.description ; Pointer to _atom_site.pdbx_auth_alt_id. ; _item.name '_atom_site_anisotrop.pdbx_auth_alt_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_auth_alt_id' _item_linked.parent_name '_atom_site.pdbx_auth_alt_id' # _item_aliases.alias_name '_atom_site_anisotrop.ndb_auth_alt_id' # _item_aliases.dictionary 'cif_rcsb.dic' # _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_auth_asym_id _item_description.description ; Pointer to _atom_site.auth_asym_id ; _item.name '_atom_site_anisotrop.pdbx_auth_asym_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_strand_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_auth_atom_id _item_description.description ; Pointer to _atom_site.auth_atom_id ; _item.name '_atom_site_anisotrop.pdbx_auth_atom_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code atcode _item_linked.child_name '_atom_site_anisotrop.pdbx_auth_atom_id' _item_linked.parent_name '_atom_site.auth_atom_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_atom_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_auth_comp_id _item_description.description ; Pointer to _atom_site.auth_comp_id ; _item.name '_atom_site_anisotrop.pdbx_auth_comp_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_residue_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_label_seq_id _item_description.description ; Pointer to _atom_site.label_seq_id ; _item.name '_atom_site_anisotrop.pdbx_label_seq_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_label_seq_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_label_alt_id _item_description.description ; Pointer to _atom_site.label_alt_id. ; _item.name '_atom_site_anisotrop.pdbx_label_alt_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_label_alt_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_label_asym_id _item_description.description ; Pointer to _atom_site.label_asym_id ; _item.name '_atom_site_anisotrop.pdbx_label_asym_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_label_atom_id _item_description.description ; Pointer to _atom_site.label_atom_id ; _item.name '_atom_site_anisotrop.pdbx_label_atom_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code atcode _item_linked.child_name '_atom_site_anisotrop.pdbx_label_atom_id' _item_linked.parent_name '_atom_site.label_atom_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_label_atom_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_label_comp_id _item_description.description ; Pointer to _atom_site.label_comp_id ; _item.name '_atom_site_anisotrop.pdbx_label_comp_id' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_atom_site_anisotrop.ndb_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site_anisotrop.pdbx_PDB_ins_code _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code ; _item.name '_atom_site_anisotrop.pdbx_PDB_ins_code' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_type.code code _item_linked.child_name '_atom_site_anisotrop.pdbx_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_atom_site_anisotrop.ndb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__cell.pdbx_unique_axis _item_description.description ; To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field. ; _item.name '_cell.pdbx_unique_axis' _item.category_id cell _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_cell.ndb_unique_axis' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__chem_comp.pdbx_synonyms _item_description.description ; Synonym list for the component. ; _item.name '_chem_comp.pdbx_synonyms' _item.category_id chem_comp _item.mandatory_code no _item_type.code line _item_examples.case ATP _item_aliases.alias_name '_chem_comp.ndb_synonyms' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__chem_comp.pdbx_modification_details _item_description.description ; For nonstandard components a text description of modification of the parent component. ; _item.name '_chem_comp.pdbx_modification_details' _item.category_id chem_comp _item.mandatory_code no _item_type.code line _item_examples.case ATP _item_aliases.alias_name '_chem_comp.rcsb_modification_details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__chem_comp.pdbx_component_no _item_description.description ; A serial number used by PDB in the FORMUL record. ; _item.name '_chem_comp.pdbx_component_no' _item.category_id chem_comp _item.mandatory_code no _item_type.code int _item_examples.case 3 _item_aliases.alias_name '_chem_comp.ndb_component_no' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__chem_comp.pdbx_type _item_description.description ; A preliminary classification used by PDB. ; _item.name '_chem_comp.pdbx_type' _item.category_id chem_comp _item.mandatory_code no _item_type.code uline save_ save__chem_comp.pdbx_formal_charge _item_description.description ; The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chem_comp.pdbx_formal_charge' _item.category_id chem_comp _item.mandatory_code no _item_default.value 0 _item_type.code int save_ save__chem_comp_atom.pdbx_align _item_description.description ; Atom name alignment offset in PDB atom field. ; _item.name '_chem_comp_atom.pdbx_align' _item.category_id chem_comp _item.mandatory_code no _item_type.code int save_ ### ### save__citation.pdbx_database_id_DOI _item_description.description ; Document Object Identifier used by doi.org to uniquely specify bibliographic entry. ; _item.name '_citation.pdbx_database_id_DOI' _item.category_id citation _item.mandatory_code no _item_type.code code _item_examples.case 'DOI:10.2345/S1384107697000225' _item_aliases.alias_name '_citation.rcsb_database_id_DOI' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__citation.pdbx_database_id_PubMed _item_description.description ; Ascession number used by PubMed to categorize a specific bibliographic entry. ; _item.name '_citation.pdbx_database_id_PubMed' _item.category_id citation _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int _item_examples.case 12627512 _item_aliases.alias_name '_citation.rcsb_database_id_PubMed' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__computing.pdbx_structure_refinement_method _item_description.description ; Program/package name for structure refinement method. ; _item.name '_computing.pdbx_structure_refinement_method' _item.category_id computing _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_computing.ndb_structure_refinement_method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__computing.pdbx_data_reduction_ii _item_description.description ; Program/package name for data reduction/intensity integration software ; _item.name '_computing.pdbx_data_reduction_ii' _item.category_id computing _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_computing.rcsb_data_reduction_ii' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__computing.pdbx_data_reduction_ds _item_description.description ; Program/package name for data reduction/data scaling ; _item.name '_computing.pdbx_data_reduction_ds' _item.category_id computing _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_computing.rcsb_data_reduction_ds' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## ## ## save__diffrn_detector.pdbx_frames_total _item_description.description ; The total number of data frames collected for this data set. ; _item.name '_diffrn_detector.pdbx_frames_total' _item.category_id diffrn_detector _item.mandatory_code no _item_type.code int loop_ _item_examples.case 20 100 save_ save__diffrn_detector.pdbx_collection_time_total _item_description.description ; The total number of seconds required to measure this data set. ; _item.name '_diffrn_detector.pdbx_collection_time_total' _item.category_id diffrn_detector _item.mandatory_code no _item_type.code float _item_units.code seconds loop_ _item_examples.case 120.0 save_ save__diffrn_detector.pdbx_collection_date _item_description.description ; The date of data collection. ; _item.name '_diffrn_detector.pdbx_collection_date' _item.category_id diffrn_detector _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case '1996-12-25' _item_aliases.alias_name '_diffrn_detector.ndb_collection_date' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__diffrn_radiation.pdbx_monochromatic_or_laue_m_l _item_description.description ; Monochromatic or Laue. ; _item.name '_diffrn_radiation.pdbx_monochromatic_or_laue_m_l' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code code _item_default.value 'M' loop_ _item_enumeration.value _item_enumeration.detail 'M' . 'L' . loop_ _item_examples.case 'M' 'L' _item_aliases.alias_name '_diffrn_radiation.ndb_monochromatic_or_laue_m_l' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__diffrn_radiation.pdbx_wavelength_list _item_description.description ; Comma separated list of wavelengths or wavelength range. ; _item.name '_diffrn_radiation.pdbx_wavelength_list' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_diffrn_source.rcsb_wavelength_list' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__diffrn_radiation.pdbx_wavelength _item_description.description ; Wavelength of radiation. ; _item.name '_diffrn_radiation.pdbx_wavelength' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_diffrn_source.rcsb_wavelength' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__diffrn_radiation.pdbx_diffrn_protocol _item_description.description ; SINGLE WAVELENGTH, LAUE, or MAD. ; _item.name '_diffrn_radiation.pdbx_diffrn_protocol' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code line _item_default.value 'SINGLE WAVELENGTH' # loop_ # _item_enumeration.value # 'SINGLE WAVELENGTH' # 'MONOCHROMATIC' # 'LAUE' # 'MAD' # 'OTHER' loop_ _item_examples.case 'SINGLE WAVELENGTH' 'MONOCHROMATIC' 'LAUE' 'MAD' 'OTHER' _item_aliases.alias_name '_diffrn_radiation.rcsb_diffrn_protocol' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__diffrn_source.pdbx_synchrotron_beamline _item_description.description ; Synchrotron beamline. ; _item.name '_diffrn_source.pdbx_synchrotron_beamline' _item.category_id diffrn_source _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_diffrn_source.ndb_synchrotron_beamline' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__diffrn_source.pdbx_synchrotron_site _item_description.description ; Synchrotron site. ; _item.name '_diffrn_source.pdbx_synchrotron_site' _item.category_id diffrn_source _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_diffrn_source.ndb_synchrotron_site' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__entity.pdbx_description _item_description.description ; A description of the entity, with the name of the entity in parenthesis. Maps to PDB compound name. ; _item.name '_entity.pdbx_description' _item.category_id entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3')' PROFLAVINE 'PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1))' _item_aliases.alias_name '_entity.ndb_description' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_number_of_molecules _item_description.description ; A place holder for the number of molecules of the entity in the entry. ; _item.name '_entity.pdbx_number_of_molecules' _item.category_id entity _item.mandatory_code no _item_type.code float loop_ _item_examples.case 1.0 2.0 3.0 _item_aliases.alias_name '_entity.ndb_number_of_molecules' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_parent_entity_id _item_description.description ; An identifier for the parent entity if this entity is part of a complex entity. For instance a chimeric entity may be decomposed into several independent chemical entities where each component entity was obtained from a different source. ; _item.name '_entity.pdbx_parent_entity_id' _item.category_id entity _item.mandatory_code no _item_type.code code _item_linked.child_name '_entity.pdbx_parent_entity_id' _item_linked.parent_name '_entity.id' loop_ _item_examples.case 1 2 3 _item_aliases.alias_name '_entity.rcsb_parent_entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_mutation _item_description.description ; Details about any entity mutation(s). ; _item.name '_entity.pdbx_mutation' _item.category_id entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Y31H' 'DEL(298-323)' _item_aliases.alias_name '_entity_keywords.ndb_mutation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_fragment _item_description.description ; Entity fragment description(s). ; _item.name '_entity.pdbx_fragment' _item.category_id entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'KLENOW FRAGMENT' 'REPLICASE OPERATOR HAIRPIN' 'C-TERMINAL DOMAIN' _item_aliases.alias_name '_entity_keywords.ndb_fragment' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_ec _item_description.description ; Enzyme Commission (EC) number(s) ; _item.name '_entity.pdbx_ec' _item.category_id entity _item.mandatory_code no _item_type.code line _item_examples.case 2.7.7.7 _item_aliases.alias_name '_entity_keywords.ndb_ec' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_modification _item_description.description ; Description(s) of any chemical or post-translational modifications ; _item.name '_entity.pdbx_modification' _item.category_id entity _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_entity_keywords.rcsb_modification' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_formula_weight_exptl _item_description.description ; Experimentally determined formula mass in daltons of the entity ; _item.name '_entity.pdbx_formula_weight_exptl' _item.category_id entity _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float _item_aliases.alias_name '_entity.rcsb_formula_weight_exptl' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_formula_weight_exptl_method _item_description.description ; Method used to determine _entity.pdbx_formula_weight_exptl. ; _item.name '_entity.pdbx_formula_weight_exptl_method' _item.category_id entity _item.mandatory_code no _item_type.code line _item_examples.case 'MASS SPEC' loop_ _item_enumeration.value 'MASS SPEC' save_ ## ## #### save__entity_keywords.pdbx_mutation _item_description.description ; Entity mutation description(s). ; _item.name '_entity_keywords.pdbx_mutation' _item.category_id entity_keywords _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Y31H' 'DEL(298-323)' # _item_aliases.alias_name '_entity_keywords.ndb_mutation' # _item_aliases.dictionary 'cif_rcsb.dic' # _item_aliases.version 1.1 _item_related.related_name '_entity.pdbx_mutation' _item_related.function_code replacedby save_ save__entity_keywords.pdbx_fragment _item_description.description ; Entity fragment description(s). ; _item.name '_entity_keywords.pdbx_fragment' _item.category_id entity_keywords _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'KLENOW FRAGMENT' 'REPLICASE OPERATOR HAIRPIN' 'C-TERMINAL DOMAIN' # _item_aliases.alias_name '_entity_keywords.ndb_fragment' # _item_aliases.dictionary 'cif_rcsb.dic' # _item_aliases.version 1.1 _item_related.related_name '_entity.pdbx_fragment' _item_related.function_code replacedby save_ save__entity_keywords.pdbx_ec _item_description.description ; Enzyme Commission (EC) number(s) ; _item.name '_entity_keywords.pdbx_ec' _item.category_id entity_keywords _item.mandatory_code no _item_type.code line _item_examples.case 2.7.7.7 # _item_aliases.alias_name '_entity_keywords.ndb_ec' # _item_aliases.dictionary 'cif_rcsb.dic' # _item_aliases.version 1.1 _item_related.related_name '_entity.pdbx_mutation' _item_related.function_code replacedby save_ ## ## save__entity_poly.pdbx_strand_id _item_description.description ; The PDB strand/chain id(s) corresponding to this polymer entity. ; _item.name '_entity_poly.pdbx_strand_id' _item.category_id entity_poly _item.mandatory_code no _item_type.code line loop_ _item_examples.case A B 'A,B,C' _item_aliases.alias_name '_entity_poly.ndb_chain_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_poly.pdbx_seq_one_letter_code _item_description.description ; Chemical sequence expressed as string of one-letter amino acid codes. Modifications and non-standard amino acids are coded as X. ; _item.name '_entity_poly.pdbx_seq_one_letter_code' _item.category_id entity_poly _item.mandatory_code no _item_type.code text _item_examples.case ; A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other ; _item_aliases.alias_name '_entity_poly.ndb_seq_one_letter_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_poly.pdbx_seq_one_letter_code_can _item_description.description ; Cannonical chemical sequence expressed as string of one-letter amino acid codes. Modifications are coded as the parent amino acid where possible. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil ; _item.name '_entity_poly.pdbx_seq_one_letter_code_can' _item.category_id entity_poly _item.mandatory_code no _item_type.code text _item_examples.case ; MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD ; _item_aliases.alias_name '_entity_poly.ndb_seq_one_letter_code_can' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_poly.pdbx_target_identifier _item_description.description ; The sequence's target identifier registered at target database. ; _item.name '_entity_poly.pdbx_target_identifier' _item.category_id entity_poly _item.mandatory_code no _item_type.code line _item_examples.case 356560 save_ ## ## save__entity_src_gen.pdbx_gene_src_fragment _item_description.description ; A domain or fragment of the molecule. ; _item.name '_entity_src_gen.pdbx_gene_src_fragment' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CYTOPLASM' 'NUCLEUS' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_fragment' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_gene _item_description.description ; Identifies the gene. ; _item.name '_entity_src_gen.pdbx_gene_src_gene' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_gene' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_scientific_name _item_description.description ; Scientific name of the organism. ; _item.name '_entity_src_gen.pdbx_gene_src_scientific_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case ; ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE ; _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_scientific_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_variant _item_description.description ; Identifies the variant. ; _item.name '_entity_src_gen.pdbx_gene_src_variant' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'DELTAH1DELTATRP' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_variant' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_cell_line _item_description.description ; The specific line of cells. ; _item.name '_entity_src_gen.pdbx_gene_src_cell_line' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'HELA CELLS' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_cell_line' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_atcc _item_description.description ; American Type Culture Collection tissue culture number. ; _item.name '_entity_src_gen.pdbx_gene_src_atcc' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case '6051' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_atcc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_organ _item_description.description ; Organized group of tissues that carries on a specialized function. ; _item.name '_entity_src_gen.pdbx_gene_src_organ' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'KIDNEY' 'LIVER' 'PANCREAS' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_organ' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_organelle _item_description.description ; Organized structure within cell. ; _item.name '_entity_src_gen.pdbx_gene_src_organelle' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'MITOCHONDRIA' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_organelle' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_plasmid _item_description.description ; The source plasmid. ; _item.name '_entity_src_gen.pdbx_gene_src_plasmid' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_plasmid' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_plasmid_name _item_description.description ; The source plasmid. ; _item.name '_entity_src_gen.pdbx_gene_src_plasmid_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_plasmid_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_cell _item_description.description ; Cell type. ; _item.name '_entity_src_gen.pdbx_gene_src_cell' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'ENDOTHELIAL' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_cell' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_gene_src_cellular_location _item_description.description ; Identifies the location inside (or outside) the cell. ; _item.name '_entity_src_gen.pdbx_gene_src_cellular_location' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CYTOPLASM' 'NUCLEUS' _item_aliases.alias_name '_entity_src_gen.ndb_gene_src_cellular_location' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_gene _item_description.description ; Specific gene which expressed the molecule. ; _item.name '_entity_src_gen.pdbx_host_org_gene' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'HIV-1 POL' 'GLNS7' 'U1A (2-98, Y31H, Q36R)' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_gene' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_organ _item_description.description ; Specific organ which expressed the molecule. ; _item.name '_entity_src_gen.pdbx_host_org_organ' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case KIDNEY _item_aliases.alias_name '_entity_src_gen.ndb_host_org_organ' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_variant _item_description.description ; Variant of the organism used as the expression system. ; _item.name '_entity_src_gen.pdbx_host_org_variant' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'TRP-LAC' 'LAMBDA DE3' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_variant' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_cell_line _item_description.description ; A specific line of cells used as the expression system. ; _item.name '_entity_src_gen.pdbx_host_org_cell_line' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'HELA' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_cell_line' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_atcc _item_description.description ; Americal Tissue Culture Collection of the expression system. ; _item.name '_entity_src_gen.pdbx_host_org_atcc' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_gen.ndb_host_org_atcc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_culture_collection _item_description.description ; Culture collection of the expression system. ; _item.name '_entity_src_gen.pdbx_host_org_culture_collection' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_gen.ndb_host_org_culture_collection' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_cell _item_description.description ; Specific cell type which expressed the molecule. ; _item.name '_entity_src_gen.pdbx_host_org_cell' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case ENDOTHELIAL _item_aliases.alias_name '_entity_src_gen.ndb_host_org_cell' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_organelle _item_description.description ; Specific organelle which expressed the molecule. ; _item.name '_entity_src_gen.pdbx_host_org_organelle' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'MITOCHONDRIA' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_organelle' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_cellular_location _item_description.description ; Identifies the location inside (or outside) the cell which expressed the molecule. ; _item.name '_entity_src_gen.pdbx_host_org_cellular_location' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CYTOPLASM' 'NUCLEUS' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_cellular_location' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_scientific_name _item_description.description ; The scientific name of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.pdbx_host_org_scientific_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case ; ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE ; _item_aliases.alias_name '_entity_src_gen.ndb_host_org_scientific_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_strain _item_description.description ; The strain of the organism in which the entity was expressed. ; _item.name '_entity_src_gen.pdbx_host_org_strain' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'AR120' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_strain' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_tissue _item_description.description ; The specific tissue which expressed the molecule. ; _item.name '_entity_src_gen.pdbx_host_org_tissue' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_tissue' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_tissue_fraction _item_description.description ; The fraction of the tissue which expressed the molecule. ; _item.name '_entity_src_gen.pdbx_host_org_tissue_fraction' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'mitochondria' 'nucleus' 'membrane' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_tissue_fraction' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_vector _item_description.description ; Identifies the vector used. ; _item.name '_entity_src_gen.pdbx_host_org_vector' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'PBIT36' 'PET15B' 'PUC18' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_vector' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_host_org_vector_type _item_description.description ; Identifies the type of vector used (plasmid, virus, or cosmid). ; _item.name '_entity_src_gen.pdbx_host_org_vector_type' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'COSMID' 'PLASMID' _item_aliases.alias_name '_entity_src_gen.ndb_host_org_vector_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_gen.pdbx_description _item_description.description ; Information on the source which is not given elsewhere. ; _item.name '_entity_src_gen.pdbx_description' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_gen.ndb_description' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__entity_src_nat.pdbx_organism_scientific _item_description.description ; Scientific name of the organism of the natural source. ; _item.name '_entity_src_nat.pdbx_organism_scientific' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'BOS TAURUS' 'SUS SCROFA' 'ASPERGILLUS ORYZAE' _item_aliases.alias_name '_entity_src_nat.ndb_organism_scientific' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_secretion _item_description.description ; Identifies the secretion from which the molecule was isolated. ; _item.name '_entity_src_nat.pdbx_secretion' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'saliva' 'urine' 'venom' _item_aliases.alias_name '_entity_src_nat.ndb_secretion' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_fragment _item_description.description ; A domain or fragment of the molecule. ; _item.name '_entity_src_nat.pdbx_fragment' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_nat.ndb_fragment' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_variant _item_description.description ; Identifies the variant. ; _item.name '_entity_src_nat.pdbx_variant' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_nat.ndb_variant' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_cell_line _item_description.description ; The specific line of cells. ; _item.name '_entity_src_nat.pdbx_cell_line' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_examples.case 'HELA' _item_aliases.alias_name '_entity_src_nat.ndb_cell_line' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_atcc _item_description.description ; Americal Tissue Culture Collection number. ; _item.name '_entity_src_nat.pdbx_atcc' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_examples.case '6051' _item_aliases.alias_name '_entity_src_nat.ndb_atcc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_cellular_location _item_description.description ; Identifies the location inside (or outside) the cell. ; _item.name '_entity_src_nat.pdbx_cellular_location' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_entity_src_nat.ndb_cellular_location' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_organ _item_description.description ; Organized group of tissues that carries on a specialized function. ; _item.name '_entity_src_nat.pdbx_organ' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_examples.case KIDNEY _item_aliases.alias_name '_entity_src_nat.ndb_organ' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_organelle _item_description.description ; Organized structure within cell. ; _item.name '_entity_src_nat.pdbx_organelle' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_examples.case MITOCHONDRIA _item_aliases.alias_name '_entity_src_nat.ndb_organelle' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_cell _item_description.description ; A particular cell type. ; _item.name '_entity_src_nat.pdbx_cell' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_examples.case 'BHK-21' _item_aliases.alias_name '_entity_src_nat.ndb_cell' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_plasmid_name _item_description.description ; The plasmid containing the gene. ; _item.name '_entity_src_nat.pdbx_plasmid_name' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_examples.case 'pB322' _item_aliases.alias_name '_entity_src_nat.ndb_plasmid_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_src_nat.pdbx_plasmid_details _item_description.description ; Details about the plasmid. ; _item.name '_entity_src_nat.pdbx_plasmid_details' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text _item_examples.case 'PLC28 DERIVATIVE' _item_aliases.alias_name '_entity_src_nat.ndb_plasmid_details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__exptl_crystal_grow.pdbx_details _item_description.description ; Text description of crystal grow procedure. ; _item.name '_exptl_crystal_grow.pdbx_details' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'PEG 4000, potassium phosphate, magnesium chloride, cacodylate' _item_aliases.alias_name '_exptl_crystal_grow.rcsb_details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__exptl_crystal_grow.pdbx_pH_range _item_description.description ; The range of pH values at which the crystal was grown. Used when a point estimate of pH is not appropriate. ; _item.name '_exptl_crystal_grow.pdbx_pH_range' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code line loop_ _item_examples.case '5.6 - 6.4' _item_aliases.alias_name '_exptl_crystal_grow.rcsb_pH_range' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__exptl_crystal.pdbx_crystal_image_url _item_description.description ; The URL for an a file containing the image of crystal. ; _item.name '_exptl_crystal.pdbx_crystal_image_url' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_exptl_crystal.rcsb_crystal_image_url' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__exptl_crystal.pdbx_crystal_image_format _item_description.description ; The image format for the file containing the image of crystal specified as an RFC2045/RFC2046 mime type. ; _item.name '_exptl_crystal.pdbx_crystal_image_format' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'jpeg' 'gif' 'tiff' _item_aliases.alias_name '_exptl_crystal.rcsb_crystal_image_format' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ################################## ## PDBX_EXPTL_CRYSTAL_GROW_COMP ## ################################## save_pdbx_exptl_crystal_grow_comp _category.description ; Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' to produce the crystal. ; _category.id pdbx_exptl_crystal_grow_comp _category.mandatory_code no loop_ _category_key.name '_pdbx_exptl_crystal_grow_comp.comp_id' '_pdbx_exptl_crystal_grow_comp.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ;loop_ _pdbx_exptl_crystal_grow_comp.crystal_id _pdbx_exptl_crystal_grow_comp.sol_id _pdbx_exptl_crystal_grow_comp.comp_id _pdbx_exptl_crystal_grow_comp.comp_name _pdbx_exptl_crystal_grow_comp.conc _pdbx_exptl_crystal_grow_comp.conc_range _pdbx_exptl_crystal_grow_comp.conc_units 4 'protein' 1 'protein' 25. . 'mg/ml' 4 'protein' 2 'Tris HCl' 20. . 'millimolar' 4 'protein' 3 'NaCl' 0.2 . 'molar' 4 'precipitant' 1 'PEG 4000' 12.5 . 'percent_weight_by_volume' 4 'precipitant' 2 'MES' 0.1 . 'molar' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_exptl_crystal_grow_comp.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_pdbx_exptl_crystal_grow_comp.crystal_id' _item.category_id pdbx_exptl_crystal_grow_comp _item.mandatory_code yes _item_linked.child_name '_pdbx_exptl_crystal_grow_comp.crystal_id' _item_linked.parent_name '_exptl_crystal.id' save_ save__pdbx_exptl_crystal_grow_comp.comp_id _item_description.description ; The value of _exptl_crystal_grow_comp.comp_id must uniquely identify each item in the PDBX_EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_pdbx_exptl_crystal_grow_comp.comp_id' _item.category_id pdbx_exptl_crystal_grow_comp _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' save_ save__pdbx_exptl_crystal_grow_comp.comp_name _item_description.description ; A common name for the component of the solution. ; _item.name '_pdbx_exptl_crystal_grow_comp.comp_name' _item.category_id pdbx_exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'protein in buffer' 'acetic acid' save_ save__pdbx_exptl_crystal_grow_comp.sol_id _item_description.description ; An identifier for the solution to which the given solution component belongs. ; _item.name '_pdbx_exptl_crystal_grow_comp.sol_id' _item.category_id pdbx_exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line _item_linked.child_name '_pdbx_exptl_crystal_grow_comp.sol_id' _item_linked.parent_name '_pdbx_exptl_crystal_grow_sol.sol_id' save_ save__pdbx_exptl_crystal_grow_comp.conc _item_description.description ; The concentration value of the solution component. ; _item.name '_pdbx_exptl_crystal_grow_comp.conc' _item.category_id pdbx_exptl_crystal_grow_comp _item.mandatory_code no _item_type.code float loop_ _item_examples.case '200.' '0.1' save_ # save__pdbx_exptl_crystal_grow_comp.conc_range _item_description.description ; The concentration range of the solution component. ; _item.name '_pdbx_exptl_crystal_grow_comp.conc_range' _item.category_id pdbx_exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case '200. - 230.' '0.1 - 0.2' save_ save__pdbx_exptl_crystal_grow_comp.conc_units _item_description.description ; The concentration units for the solution component. ; _item.name '_pdbx_exptl_crystal_grow_comp.conc_units' _item.category_id pdbx_exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'millimolar' 'percent_weight_by_volume' 'milligrams_per_milliliter' save_ ## ## ############################ ## PDBX_EXPTL_CRYSTAL_SOL ## ############################ save_pdbx_exptl_crystal_grow_sol _category.description ; Data items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record details about the solutions that were 'mixed' to produce the crystal. ; _category.id pdbx_exptl_crystal_grow_sol _category.mandatory_code no loop_ _category_key.name '_pdbx_exptl_crystal_grow_sol.sol_id' '_pdbx_exptl_crystal_grow_sol.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case ; Example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _pdbx_exptl_crystal_grow_sol.crystal_id _pdbx_exptl_crystal_grow_sol.sol_id _pdbx_exptl_crystal_grow_sol.volume _pdbx_exptl_crystal_grow_sol.volume_units _pdbx_exptl_crystal_grow_sol.pH 1 'protein' 0.5 'microliter' 7.5 1 'precipitant' 0.5 'microliter' 7.3 1 'reservoir' 0.5 'milliliter' 7.3 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_exptl_crystal_grow_sol.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_pdbx_exptl_crystal_grow_sol.crystal_id' _item.category_id pdbx_exptl_crystal_grow_sol _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_exptl_crystal_grow_sol.crystal_id' _item_linked.parent_name '_exptl_crystal.id' save_ save__pdbx_exptl_crystal_grow_sol.sol_id _item_description.description ; An identifier for this solution (e.g. precipitant, reservoir, macromolecule) ; _item.name '_pdbx_exptl_crystal_grow_sol.sol_id' _item.category_id pdbx_exptl_crystal_grow_sol _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value "precipitant" "reservoir" "macromolecule" save_ save__pdbx_exptl_crystal_grow_sol.volume _item_description.description ; The volume of the solution. ; _item.name '_pdbx_exptl_crystal_grow_sol.volume' _item.category_id pdbx_exptl_crystal_grow_sol _item.mandatory_code no _item_type.code float loop_ _item_examples.case '200.' '0.1' save_ save__pdbx_exptl_crystal_grow_sol.volume_units _item_description.description ; The volume units of the solution. ; _item.name '_pdbx_exptl_crystal_grow_sol.volume_units' _item.category_id pdbx_exptl_crystal_grow_sol _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'milliliter' 'micoliter' save_ save__pdbx_exptl_crystal_grow_sol.pH _item_description.description ; The pH of the solution. ; _item.name '_pdbx_exptl_crystal_grow_sol.pH' _item.category_id pdbx_exptl_crystal_grow_sol _item.mandatory_code no _item_type.code float loop_ _item_examples.case '7.2' save_ ## ## ####################################### ## PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT ## ####################################### save_pdbx_exptl_crystal_cryo_treatment _category.description ; Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category record details cryogenic treatments applied to this crystal. ; _category.id pdbx_exptl_crystal_cryo_treatment _category.mandatory_code no loop_ _category_key.name '_pdbx_exptl_crystal_cryo_treatment.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case ; Example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _pdbx_exptl_crystal_cryo_treatment.crystal_id 4 _pdbx_exptl_crystal_cryo_treatment.final_solution_details ; 25% (v/v) glycerol in precipitant solution ; _pdbx_exptl_crystal_cryo_treatment.soaking_details ; A series of 1 min soaks beginning at 5% (v/v) glycerol in precipitant, transiting to 20% (v/v) glycerol, and finally to 25% glycerol ; _pdbx_exptl_crystal_cryo_treatment.cooling_details ; Direct immersion in liquid nitrogen ; _pdbx_exptl_crystal_cryo_treatment.annealing_details ? ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_exptl_crystal_cryo_treatment.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_pdbx_exptl_crystal_cryo_treatment.crystal_id' _item.category_id pdbx_exptl_crystal_cryo_treatment _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_exptl_crystal_cryo_treatment.crystal_id' _item_linked.parent_name '_exptl_crystal.id' save_ save__pdbx_exptl_crystal_cryo_treatment.final_solution_details _item_description.description ; Details of the final solution used in the treatment of this crystal ; _item.name '_pdbx_exptl_crystal_cryo_treatment.final_solution_details' _item.category_id pdbx_exptl_crystal_cryo_treatment _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; 25% (v/v) glycerol in precipitant solution ; save_ save__pdbx_exptl_crystal_cryo_treatment.soaking_details _item_description.description ; Details of the soaking treatment applied to this crystal. ; _item.name '_pdbx_exptl_crystal_cryo_treatment.soaking_details' _item.category_id pdbx_exptl_crystal_cryo_treatment _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; A series of 1 min soaks beginning at 5% (v/v) glycerol in precipitant, transiting to 20% (v/v) glycerol, and finally to 25% glycerol ; save_ save__pdbx_exptl_crystal_cryo_treatment.cooling_details _item_description.description ; Details of the cooling treatment applied to this crystal. ; _item.name '_pdbx_exptl_crystal_cryo_treatment.cooling_details' _item.category_id pdbx_exptl_crystal_cryo_treatment _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; Direct immersion in liquid nitrogen ; save_ save__pdbx_exptl_crystal_cryo_treatment.annealing_details _item_description.description ; Details of the annealing treatment applied to this crystal. ; _item.name '_pdbx_exptl_crystal_cryo_treatment.annealing_details' _item.category_id pdbx_exptl_crystal_cryo_treatment _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; 10 sec interruption of cold stream with plastic ruler. Performed twice. ; save_ ## save__geom_angle.pdbx_atom_site_PDB_ins_code_1 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_angle.pdbx_atom_site_PDB_ins_code_1' _item.category_id geom_angle _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_angle.pdbx_atom_site_PDB_ins_code_1' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_angle.ndb_atom_site_PDB_ins_code_1' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_angle.pdbx_atom_site_PDB_ins_code_2 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_angle.pdbx_atom_site_PDB_ins_code_2' _item.category_id geom_angle _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_angle.pdbx_atom_site_PDB_ins_code_2' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_angle.ndb_atom_site_PDB_ins_code_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_angle.pdbx_atom_site_PDB_ins_code_3 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_angle.pdbx_atom_site_PDB_ins_code_3' _item.category_id geom_angle _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_angle.pdbx_atom_site_PDB_ins_code_3' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_angle.ndb_atom_site_PDB_ins_code_3' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_angle.pdbx_PDB_model_num _item_description.description ; Pointer to _atom_site.pdbx_PDB_model_num ; _item.name '_geom_angle.pdbx_PDB_model_num' _item.category_id geom_angle _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_angle.pdbx_PDB_model_num' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' _item_aliases.alias_name '_geom_angle.ndb_model_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_bond.pdbx_atom_site_PDB_ins_code_1 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_bond.pdbx_atom_site_PDB_ins_code_1' _item.category_id geom_bond _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_bond.pdbx_atom_site_PDB_ins_code_1' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_bond.ndb_atom_site_PDB_ins_code_1' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_bond.pdbx_atom_site_PDB_ins_code_2 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_bond.pdbx_atom_site_PDB_ins_code_2' _item.category_id geom_bond _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_bond.pdbx_atom_site_PDB_ins_code_2' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_bond.ndb_atom_site_PDB_ins_code_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_bond.pdbx_PDB_model_num _item_description.description ; Pointer to _atom_site.pdbx_PDB_model_num ; _item.name '_geom_bond.pdbx_PDB_model_num' _item.category_id geom_bond _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_bond.pdbx_PDB_model_num' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' _item_aliases.alias_name '_geom_bond.ndb_model_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_contact.pdbx_atom_site_PDB_ins_code_1 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_contact.pdbx_atom_site_PDB_ins_code_1' _item.category_id geom_contact _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_contact.pdbx_atom_site_PDB_ins_code_1' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_contact.ndb_atom_site_PDB_ins_code_1' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_contact.pdbx_atom_site_PDB_ins_code_2 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_contact.pdbx_atom_site_PDB_ins_code_2' _item.category_id geom_contact _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_contact.pdbx_atom_site_PDB_ins_code_2' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_contact.ndb_atom_site_PDB_ins_code_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_contact.pdbx_PDB_model_num _item_description.description ; Pointer to _atom_site.pdbx_PDB_model_num ; _item.name '_geom_contact.pdbx_PDB_model_num' _item.category_id geom_contact _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_contact.pdbx_PDB_model_num' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' _item_aliases.alias_name '_geom_contact.ndb_model_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_torsion.pdbx_atom_site_PDB_ins_code_1 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_1' _item.category_id geom_torsion _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_1' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_1' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_torsion.pdbx_atom_site_PDB_ins_code_2 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_2' _item.category_id geom_torsion _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_2' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_torsion.pdbx_atom_site_PDB_ins_code_3 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_3' _item.category_id geom_torsion _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_3' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_3' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_torsion.pdbx_atom_site_PDB_ins_code_4 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_4' _item.category_id geom_torsion _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_4' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_4' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__geom_torsion.pdbx_PDB_model_num _item_description.description ; Pointer to _atom_site.pdbx_PDB_model_num ; _item.name '_geom_torsion.pdbx_PDB_model_num' _item.category_id geom_torsion _item.mandatory_code no _item_type.code code _item_linked.child_name '_geom_torsion.pdbx_PDB_model_num' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' _item_aliases.alias_name '_geom_torsion.ndb_model_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__refine.pdbx_ls_sigma_I _item_description.description ; Data cutoff (SIGMA(I)) ; _item.name '_refine.pdbx_ls_sigma_I' _item.category_id refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_refine.ndb_ls_sigma_I' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_ls_sigma_F _item_description.description ; Data cutoff (SIGMA(F)) ; _item.name '_refine.pdbx_ls_sigma_F' _item.category_id refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_refine.ndb_ls_sigma_F' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_ls_sigma_Fsqd _item_description.description ; Data cutoff (SIGMA(F^2)) ; _item.name '_refine.pdbx_ls_sigma_Fsqd' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.pdbx_data_cutoff_high_absF _item_description.description ; Value of F at "high end" of data cutoff. ; _item.name '_refine.pdbx_data_cutoff_high_absF' _item.category_id refine _item.mandatory_code no _item_type.code float _item_examples.case 17600 _item_aliases.alias_name '_refine.ndb_data_cutoff_high_absF' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_data_cutoff_high_rms_absF _item_description.description ; Value of RMS |F| used as high data cutoff. ; _item.name '_refine.pdbx_data_cutoff_high_rms_absF' _item.category_id refine _item.mandatory_code no _item_type.code float _item_examples.case 205.1 _item_aliases.alias_name '_refine.rcsb_data_cutoff_high_rms_absF' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_data_cutoff_low_absF _item_description.description ; Value of F at "low end" of data cutoff. ; _item.name '_refine.pdbx_data_cutoff_low_absF' _item.category_id refine _item.mandatory_code no _item_type.code float _item_examples.case 0.30 _item_aliases.alias_name '_refine.ndb_data_cutoff_low_absF' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_isotropic_thermal_model _item_description.description ; Whether the structure was refined with indvidual isotropic, anisotropic or overall temperature factor. ; _item.name '_refine.pdbx_isotropic_thermal_model' _item.category_id refine _item.mandatory_code no _item_type.code text loop_ _item_examples.case Isotropic Overall _item_aliases.alias_name '_refine.ndb_isotropic_thermal_model' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_ls_cross_valid_method _item_description.description ; Whether the cross validataion method was used through out or only at the end. ; _item.name '_refine.pdbx_ls_cross_valid_method' _item.category_id refine _item.mandatory_code no _item_type.code text _item_examples.case 'FREE R-VALUE' _item_aliases.alias_name '_refine.ndb_ls_cross_valid_method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_method_to_determine_struct _item_description.description ; Method(s) used to determine the structure. ; _item.name '_refine.pdbx_method_to_determine_struct' _item.category_id refine _item.mandatory_code no _item_type.code text loop_ _item_examples.case _item_examples.detail 'AB INITIO PHASING' ? 'DM' 'Direct Methods' 'ISAS ' 'Iterative Single wavelength Anomalous Scattering' 'ISIR' 'Iterative Single Isomorphous Replacement' 'ISIRAS' 'Iterative Single Isomorphous Replacement with Anomalous Scattering' 'MAD' 'Multi wavelength Anomalous Diffraction' 'MIR' 'Multiple Isomorphous Replacement' 'MIRAS' 'Multiple Isomorphous Replacement with Anomalous Scattering' 'MR' 'Molecular Replacement' 'SIR' 'Single Isomorphous Replacement' 'SIRAS' 'Single Isomorphous Replacement with Anomalous Scattering' _item_aliases.alias_name '_refine.ndb_method_to_determine_struct' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_starting_model _item_description.description ; Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment. ; _item.name '_refine.pdbx_starting_model' _item.category_id refine _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'BDL001' _item_aliases.alias_name '_refine.ndb_starting_model' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_stereochemistry_target_values _item_description.description ; Stereochemistry target values used in refinement. ; _item.name '_refine.pdbx_stereochemistry_target_values' _item.category_id refine _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_refine.ndb_stereochemistry_target_values' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_R_Free_selection_details _item_description.description ; Details of the manner in which the cross validation reflections were selected. ; _item.name '_refine.pdbx_R_Free_selection_details' _item.category_id refine _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Random selection' _item_aliases.alias_name '_refine.ndb_R_Free_selection_details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine.pdbx_stereochem_target_val_spec_case _item_description.description ; Special case of stereochemistry target values used in SHELXL refinement. ; _item.name '_refine.pdbx_stereochem_target_val_spec_case' _item.category_id refine _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_refine.ndb_stereochem_target_val_spec_case' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_hist.pdbx_number_atoms_protein _item_description.description ; Number of protein atoms included in refinement ; _item.name '_refine_hist.pdbx_number_atoms_protein' _item.category_id refine_hist _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_refine_hist.rcsb_number_atoms_protein' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_hist.pdbx_number_atoms_nucleic_acid _item_description.description ; Number of nucleic atoms included in refinement ; _item.name '_refine_hist.pdbx_number_atoms_nucleic_acid' _item.category_id refine_hist _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_refine_hist.rcsb_number_atoms_nucleic_acid' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_hist.pdbx_number_atoms_ligand _item_description.description ; Number of ligand atoms included in refinement ; _item.name '_refine_hist.pdbx_number_atoms_ligand' _item.category_id refine_hist _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_refine_hist.rcsb_number_atoms_ligand' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ # save__refine_hist.pdbx_number_atoms_lipid _item_description.description ; Number of lipid atoms included in refinement ; _item.name '_refine_hist.pdbx_number_atoms_lipid' _item.category_id refine_hist _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_refine_hist.rcsb_number_atoms_lipid' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_hist.pdbx_number_atoms_carb _item_description.description ; Number of carbohydrate atoms included in refinement ; _item.name '_refine_hist.pdbx_number_atoms_carb' _item.category_id refine_hist _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_refine_hist.rcsb_number_atoms_carb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_hist.pdbx_pseudo_atom_details _item_description.description ; Details of pseduo atoms used to model unexplained density ; _item.name '_refine_hist.pdbx_pseudo_atom_details' _item.category_id refine_hist _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_refine_hist.rcsb_pseudo_atom_details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ### save__refine_ls_shell.pdbx_total_number_of_bins_used _item_description.description ; Total number of bins used. ; _item.name '_refine_ls_shell.pdbx_total_number_of_bins_used' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_refine_ls_shell.ndb_total_number_of_bins_used' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__refln.pdbx_F_calc_part_solvent _item_description.description ; The calculated value of the structure factor in arbitrary units reflecting only the contribution of the solvent model. ; _item.name '_refln.pdbx_F_calc_part_solvent' _item.category_id refln _item.mandatory_code no _item_type.code float _item_units.code arbitrary _item_aliases.alias_name '_refln.rcsb_F_calc_part_solvent' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refln.pdbx_phase_calc_part_solvent _item_description.description ; The calculated structure-factor phase in degrees reflecting only the contribution of the solvent model. ; _item.name '_refln.pdbx_phase_calc_part_solvent' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln.rcsb_phase_calc_part_solvent' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_type.code float _item_units.code degrees save_ save__refln.pdbx_F_calc_with_solvent _item_description.description ; The calculated value of the structure factor in arbitrary units including the contribution of the solvent model. ; _item.name '_refln.pdbx_F_calc_with_solvent' _item.category_id refln _item.mandatory_code no _item_type.code float _item_units.code arbitrary _item_aliases.alias_name '_refln.rcsb_F_calc_with_solvent' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refln.pdbx_phase_calc_with_solvent _item_description.description ; The calculated structure-factor phase in degrees including the contribution of the solvent model. ; _item.name '_refln.pdbx_phase_calc_with_solvent' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln.rcsb_phase_calc_with_solvent' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_type.code float _item_units.code degrees save_ ## ## save__reflns.pdbx_redundancy _item_description.description ; Overall redundancy for this data set (%). ; _item.name '_reflns.pdbx_redundancy' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_reflns.ndb_redundancy' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns.pdbx_Rmerge_I_obs _item_description.description ; The R value for merging intensities satisfying the observed criteria in this data set. ; _item.name '_reflns.pdbx_Rmerge_I_obs' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_reflns.ndb_Rmerge_I_obs' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns.pdbx_Rmerge_I_all _item_description.description ; The R value for merging all intensities in this data set. ; _item.name '_reflns.pdbx_Rmerge_I_all' _item.category_id reflns _item.mandatory_code no _item_type.code float save_ save__reflns.pdbx_Rsym_value _item_description.description ; R Sym value in percent. ; _item.name '_reflns.pdbx_Rsym_value' _item.category_id reflns _item.mandatory_code no _item_examples.case 2.0 _item_type.code float _item_aliases.alias_name '_reflns.ndb_Rsym_value' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns.pdbx_netI_over_av_sigmaI _item_description.description ; Overall / ; _item.name '_reflns.pdbx_netI_over_av_sigmaI' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_reflns.ndb_netI_over_av_sigmaI' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns.pdbx_netI_over_sigmaI _item_description.description ; Overall ; _item.name '_reflns.pdbx_netI_over_sigmaI' _item.category_id reflns _item.mandatory_code no _item_type.code float save_ save__reflns.pdbx_res_netI_over_av_sigmaI_2 _item_description.description ; Resolution (angstrom) for reflections with / = 2. ; _item.name '_reflns.pdbx_res_netI_over_av_sigmaI_2' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__reflns.pdbx_res_netI_over_sigmaI_2 _item_description.description ; Resolution (angstroms) for reflections with = 2. ; _item.name '_reflns.pdbx_res_netI_over_sigmaI_2' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__reflns.pdbx_chi_squared _item_description.description ; Overall Chi-squared statistic. ; _item.name '_reflns.pdbx_chi_squared' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_reflns.rcsb_chi_squared' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns.pdbx_scaling_rejects _item_description.description ; Number of reflections rejected in scaling operations. ; _item.name '_reflns.pdbx_scaling_rejects' _item.category_id reflns _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_reflns.rcsb_scaling_rejects' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns.pdbx_d_res_high_opt _item_description.description ; The highest optical resolution for this reflection data set as determined by computational method _reflns.pdbx_d_res_opt_method. ; _item.name '_reflns.pdbx_d_res_high_opt' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns.rcsb_d_res_high_opt' _item_aliases.dictionary cif_rcsb.dic _item_aliases.version 1.1 _item_examples.case '1.2' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns.pdbx_d_res_low_opt _item_description.description ; The lowest optical resolution for this reflection data set as determined by computational method _reflns.pdbx_d_res_opt_method. ; _item.name '_reflns.pdbx_d_res_low_opt' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns.rcsb_d_res_low_opt' _item_aliases.dictionary cif_rcsb.dic _item_aliases.version 1.1 _item_examples.case '20.5' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns.pdbx_d_res_opt_method _item_description.description ; The computational method used to determine the optical resolution limits _reflns.pdbx_d_res_high_opt and _reflns.pdbx_d_res_low_opt. ; _item.name '_reflns.pdbx_d_res_opt_method' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns.rcsb_d_res_opt_method' _item_aliases.dictionary cif_rcsb.dic _item_aliases.version 1.1 _item_examples.case 'SFCHECK' _item_type.code text save_ ## ## save__reflns_shell.pdbx_redundancy _item_description.description ; Redundancy for the current shell. ; _item.name '_reflns_shell.pdbx_redundancy' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_reflns_shell.ndb_redundancy' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns_shell.pdbx_Rsym_value _item_description.description ; R sym value in percent. ; _item.name '_reflns_shell.pdbx_Rsym_value' _item.category_id reflns_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_aliases.alias_name '_reflns_shell.ndb_Rsym_value' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns_shell.pdbx_chi_squared _item_description.description ; Chi-squared statistic for this resolution shell. ; _item.name '_reflns_shell.pdbx_chi_squared' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_reflns_shell.rcsb_chi_squared' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__reflns_shell.pdbx_netI_over_sigmaI_all _item_description.description ; The mean of the ratio of the intensities to their standard uncertainties of all reflections in the resolution shell. _reflns_shell.pdbx_meanI_over_sigmaI_all = ; _item.name '_reflns_shell.pdbx_netI_over_sigmaI_all' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float save_ save__reflns_shell.pdbx_netI_over_sigmaI_obs _item_description.description ; The mean of the ratio of the intensities to their standard uncertainties of observed reflections (see _reflns.observed_criterion) in the resolution shell. _reflns_shell.pdbx_meanI_over_sigmaI_obs = ; _item.name '_reflns_shell.pdbx_netI_over_sigmaI_obs' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float save_ ## save__struct.pdbx_descriptor _item_description.description ; An automatically generated descriptor for an NDB structure or the unstructured content of the PDB COMPND record. ; _item.name '_struct.pdbx_descriptor' _item.category_id struct _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3' ; _item_aliases.alias_name '_struct.ndb_descriptor' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct.pdbx_model_details _item_description.description ; Text description of the methodology which produced this model structure. ; _item.name '_struct.pdbx_model_details' _item.category_id struct _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; This model was produced from a 10 nanosecond Amber/MD simulation starting from PDB structure ID 1ABC. ; _item_aliases.alias_name '_struct.rcsb_model_details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct.pdbx_formula_weight _item_description.description ; Estimated formula mass in daltons of the deposited structure assembly. ; _item.name '_struct.pdbx_formula_weight' _item.category_id struct _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__struct.pdbx_formula_weight_method _item_description.description ; Method used to determine _struct.pdbx_formula_weight. ; _item.name '_struct.pdbx_formula_weight_method' _item.category_id struct _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'MASS SPEC' 'CALCULATION' save_ ## save__struct_asym.pdbx_modified _item_description.description ; This data item indicates whether the structural elements are modified. ; _item.name '_struct_asym.pdbx_modified' _item.category_id struct_asym _item.mandatory_code no _item_type.code text _item_examples.case 'y' _item_aliases.alias_name '_struct_asym.ndb_modified' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_asym.pdbx_blank_PDB_chainid_flag _item_description.description ; A flag indicating that this entity was originally labeled with a blank PDB chain id. ; _item.name '_struct_asym.pdbx_blank_PDB_chainid_flag' _item.category_id struct_asym _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail Y 'Yes' N 'No' _item_aliases.alias_name '_struct_asym.rcsb_blank_PDB_chainid_flag' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_biol.pdbx_parent_biol_id _item_description.description ; An identifier for the parent biological assembly if this biological unit is part of a complex assembly. ; _item.name '_struct_biol.pdbx_parent_biol_id' _item.category_id struct_biol _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_biol.pdbx_parent_biol_id' _item_linked.parent_name '_struct_biol.id' loop_ _item_examples.case 1 2 3 _item_aliases.alias_name '_struct_biol.rcsb_parent_biol_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_biol.pdbx_formula_weight _item_description.description ; Estimated formula mass in daltons of the biological assembly. ; _item.name '_struct_biol.pdbx_formula_weight' _item.category_id struct_biol _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__struct_biol.pdbx_formula_weight_method _item_description.description ; Method used to determine _struct_biol.pdbx_formula_weight. ; _item.name '_struct_biol.pdbx_formula_weight_method' _item.category_id struct_biol _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'MASS SPEC' 'CALCULATION' save_ ## ## save__struct_biol_gen.pdbx_full_symmetry_operation _item_description.description ; This item expresses category _struct_biol_gen.symmetry on an X, Y and Z basis. ; _item.name '_struct_biol_gen.pdbx_full_symmetry_operation' _item.category_id struct_biol_gen _item.mandatory_code no _item_type.code code _item_examples.case '-X, Y+1/2, -Z' _item_aliases.alias_name '_struct_biol_gen.ndb_full_symmetry_operation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_biol_gen.pdbx_PDB_order _item_description.description ; An ordering index used to reproduce the presentation of chain order in the original PDB format data files. ; _item.name '_struct_biol_gen.pdbx_PDB_order' _item.category_id struct_biol_gen _item.mandatory_code no _item_type.code int loop_ _item_examples.case 1 2 3 _item_aliases.alias_name '_struct_biol_gen.rcsb_pdb_order' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_conf.pdbx_beg_PDB_ins_code _item_description.description ; A component of the identifier for the residue at which the conformation segment starts. ; _item.name '_struct_conf.pdbx_beg_PDB_ins_code' _item.category_id struct_conf _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_conf.pdbx_beg_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_conf.ndb_beg_label_ins_code_pdb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conf.pdbx_end_PDB_ins_code _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. ; _item.name '_struct_conf.pdbx_end_PDB_ins_code' _item.category_id struct_conf _item.mandatory_code no _item_linked.child_name '_struct_conf.pdbx_end_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_conf.ndb_end_label_ins_code_pdb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conf.pdbx_PDB_helix_class _item_description.description ; This item is a place holder for the helix class used in the PDB HELIX record. ; _item.name '_struct_conf.pdbx_PDB_helix_class' _item.category_id struct_conf _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_struct_conf.ndb_helix_class_pdb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conf.pdbx_PDB_helix_length _item_description.description ; A placeholder for the lengths of the helix of the PDB HELIX record. ; _item.name '_struct_conf.pdbx_PDB_helix_length' _item.category_id struct_conf _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_struct_conf.ndb_length' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conf.pdbx_PDB_helix_id _item_description.description ; A placeholder for the helix identifier of the PDB HELIX record. ; _item.name '_struct_conf.pdbx_PDB_helix_id' _item.category_id struct_conf _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_struct_conf.pdb_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_conn.pdbx_ptnr1_PDB_ins_code _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.ins_code in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr1_PDB_ins_code' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_linked.child_name '_struct_conn.pdbx_ptnr1_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_conn.ndb_ptnr1_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr1_auth_alt_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.pdbx_auth_alt_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr1_auth_alt_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_linked.child_name '_struct_conn.pdbx_ptnr1_auth_alt_id' _item_linked.parent_name '_atom_site.pdbx_auth_alt_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr1_auth_alt_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr1_label_alt_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr1_label_alt_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_linked.child_name '_struct_conn.pdbx_ptnr1_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr1_label_alt_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr1_standard_comp_id _item_description.description ; A placeholder for the standard residue name found in the MODRES record of a PDB file. ; _item.name '_struct_conn.pdbx_ptnr1_standard_comp_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'T' 'C' 'G' 'GLY' 'ALA' 'MET' _item_aliases.alias_name '_struct_conn.ndb_ptnr1_standard_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr2_PDB_ins_code _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr2_PDB_ins_code' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_linked.child_name '_struct_conn.pdbx_ptnr2_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_conn.ndb_ptnr2_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr2_auth_alt_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.pdbx_auth_alt_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr2_auth_alt_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_linked.child_name '_struct_conn.pdbx_ptnr2_auth_alt_id' _item_linked.parent_name '_atom_site.pdbx_auth_alt_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr2_auth_alt_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr2_label_alt_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr2_label_alt_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_linked.child_name '_struct_conn.pdbx_ptnr2_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr2_label_alt_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_auth_alt_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.auth_alt_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_auth_alt_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_alt_id' _item_linked.parent_name '_atom_site.pdbx_auth_alt_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_alt_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_auth_asym_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_auth_asym_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' 'C' _item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_auth_atom_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_auth_atom_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code atcode _item_examples.case 'O5*' _item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_atom_id' _item_linked.parent_name '_atom_site.auth_atom_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_atom_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_auth_comp_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_auth_comp_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'T' 'C' 'G' 'GLY' 'ALA' 'MET' _item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_PDB_ins_code _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_PDB_ins_code' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_linked.child_name '_struct_conn.pdbx_ptnr3_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_auth_seq_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_auth_seq_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code _item_examples.case '12' _item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__struct_conn.pdbx_ptnr3_label_alt_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_label_alt_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_linked.child_name '_struct_conn.pdbx_ptnr3_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_alt_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_label_asym_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_label_asym_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' 'C' _item_linked.child_name '_struct_conn.pdbx_ptnr3_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_label_atom_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_label_atom_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code atcode _item_examples.case 'O5*' _item_linked.child_name '_struct_conn.pdbx_ptnr3_label_atom_id' _item_linked.parent_name '_atom_site.label_atom_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_atom_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_label_comp_id _item_description.description ; A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_label_comp_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'T' 'C' 'G' 'GLY' 'ALA' 'MET' _item_linked.child_name '_struct_conn.pdbx_ptnr3_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conn.pdbx_ptnr3_label_seq_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.pdbx_ptnr3_label_seq_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code _item_examples.case '12' _item_linked.child_name '_struct_conn.pdbx_ptnr3_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' _item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__struct_conn.pdbx_PDB_id _item_description.description ; A placeholder for the PDB id in the case the category is used to hold the information of the MODRES record of a PDB file. ; _item.name '_struct_conn.pdbx_PDB_id' _item.category_id struct_conn _item.mandatory_code no _item_type.code code _item_examples.case 1ABC _item_aliases.alias_name '_struct_conn.ndb_PDB_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_keywords.pdbx_keywords _item_description.description ; ; _item.name '_struct_keywords.pdbx_keywords' _item.category_id struct_keywords _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'DNA' 'RNA' 'T-RNA' 'DNA/RNA' 'RIBOZYME' 'PROTEIN/DNA' 'PROTEIN/RNA' 'PEPTIDE NUCLEIC ACID' 'PEPTIDE NUCLEIC ACID/DNA' 'DNA-BINDING PROTEIN' 'RNA-BINDING PROTEIN' _item_aliases.alias_name '_struct_keywords.ndb_keywords' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## ## save__struct_mon_prot_cis.pdbx_auth_asym_id_2 _item_description.description ; Pointer to _atom_site.auth_asym_id. ; _item.name '_struct_mon_prot_cis.pdbx_auth_asym_id_2' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_auth_asym_id_2' _item_linked.parent_name '_atom_site.auth_asym_id' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_auth_asym_id_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_auth_comp_id_2 _item_description.description ; Pointer to _atom_site.auth_comp_id. ; _item.name '_struct_mon_prot_cis.pdbx_auth_comp_id_2' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_auth_comp_id_2' _item_linked.parent_name '_atom_site.auth_comp_id' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_auth_comp_id_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_auth_seq_id_2 _item_description.description ; Pointer to _atom_site.auth_seq_id ; _item.name '_struct_mon_prot_cis.pdbx_auth_seq_id_2' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_auth_seq_id_2' _item_linked.parent_name '_atom_site.auth_seq_id' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_auth_seq_id_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ##jdw save__struct_mon_prot_cis.pdbx_label_asym_id_2 _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_struct_mon_prot_cis.pdbx_label_asym_id_2' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_label_asym_id_2' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_asym_id_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_label_comp_id_2 _item_description.description ; Pointer to _atom_site.label_comp_id. ; _item.name '_struct_mon_prot_cis.pdbx_label_comp_id_2' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_label_comp_id_2' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_comp_id_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_label_seq_id_2 _item_description.description ; Pointer to _atom_site.label_seq_id ; _item.name '_struct_mon_prot_cis.pdbx_label_seq_id_2' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_label_seq_id_2' _item_linked.parent_name '_atom_site.label_seq_id' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_seq_id_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_PDB_ins_code _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code ; _item.name '_struct_mon_prot_cis.pdbx_PDB_ins_code' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_PDB_ins_code_2 _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code ; _item.name '_struct_mon_prot_cis.pdbx_PDB_ins_code_2' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_PDB_ins_code_2' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_ins_code_2' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_PDB_model_num _item_description.description ; Pointer to _atom_site.pdbx_PDB_model_num ; _item.name '_struct_mon_prot_cis.pdbx_PDB_model_num' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_mon_prot_cis.pdbx_PDB_model_num' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' _item_aliases.alias_name '_struct_mon_prot_cis.ndb_model_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_omega_angle _item_description.description ; omega torsion angle ; _item.name '_struct_mon_prot_cis.pdbx_omega_angle' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_struct_mon_prot_cis.ndb_omega_angle' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_mon_prot_cis.pdbx_id _item_description.description ; ordinal index ; _item.name '_struct_mon_prot_cis.pdbx_id' _item.category_id struct_mon_prot_cis _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_struct_mon_prot_cis.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_ref.pdbx_db_accession _item_description.description ; Accession code of the reference database. ; _item.name '_struct_ref.pdbx_db_accession' _item.category_id struct_ref _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'P07617' _item_aliases.alias_name '_struct_ref.rcsb_db_accession' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref.pdbx_seq_one_letter_code _item_description.description ; Database chemical sequence expressed as string of one-letter amino acid codes. ; _item.name '_struct_ref.pdbx_seq_one_letter_code' _item.category_id struct_ref _item.mandatory_code no _item_type.code text _item_examples.case ; A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other ; _item_aliases.alias_name '_struct_ref.rcsb_seq_one_letter_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref.pdbx_align_begin _item_description.description ; Beginning index in the chemical sequence from the reference database. ; _item.name '_struct_ref.pdbx_align_begin' _item.category_id struct_ref _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref.rcsb_align_begin' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_ref_seq.pdbx_strand_id _item_description.description ; The PDB strand/chain ID . ; _item.name '_struct_ref_seq.pdbx_strand_id' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_aliases.alias_name '_struct_ref_seq.ndb_chain_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_db_accession _item_description.description ; Accession code of the reference database. ; _item.name '_struct_ref_seq.pdbx_db_accession' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'P07617' _item_aliases.alias_name '_struct_ref_seq.ndb_db_accession' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_db_align_beg_ins_code _item_description.description ; Initial insertion code of the sequence segment of the reference database. ; _item.name '_struct_ref_seq.pdbx_db_align_beg_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_db_align_beg_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_db_align_end_ins_code _item_description.description ; Ending insertion code of the sequence segment of the reference database. ; _item.name '_struct_ref_seq.pdbx_db_align_end_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_db_align_end_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_PDB_id_code _item_description.description ; The PDB code of the structure. ; _item.name '_struct_ref_seq.pdbx_PDB_id_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code _item_examples.case '1BBP' _item_aliases.alias_name '_struct_ref_seq.ndb_pdb_id_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_auth_seq_align_beg _item_description.description ; Initial position in the PDB sequence segment. ; _item.name '_struct_ref_seq.pdbx_auth_seq_align_beg' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_auth_seq_align_beg' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_auth_seq_align_end _item_description.description ; Ending position in the PDB sequence segment ; _item.name '_struct_ref_seq.pdbx_auth_seq_align_end' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_auth_seq_align_end' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__struct_ref_seq.pdbx_seq_align_beg_ins_code _item_description.description ; Initial insertion code of the PDB sequence segment. ; _item.name '_struct_ref_seq.pdbx_seq_align_beg_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_seq_align_beg_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_seq_align_end_ins_code _item_description.description ; Ending insertion code of the sequence segment ; _item.name '_struct_ref_seq.pdbx_seq_align_end_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_seq_align_end_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_ref_seq_dif.pdbx_pdb_id_code _item_description.description ; The PDB ID code. ; _item.name '_struct_ref_seq_dif.pdbx_pdb_id_code' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code code _item_examples.case '1BBP' _item_aliases.alias_name '_struct_ref_seq_dif.ndb_pdb_id_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq_dif.pdbx_pdb_strand_id _item_description.description ; PDB strand/chain id. ; _item.name '_struct_ref_seq_dif.pdbx_pdb_strand_id' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_aliases.alias_name '_struct_ref_seq_dif.ndb_pdb_chain_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq_dif.pdbx_pdb_ins_code _item_description.description ; Insertion code in PDB sequence ; _item.name '_struct_ref_seq_dif.pdbx_pdb_ins_code' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq_dif.ndb_pdb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq_dif.pdbx_auth_seq_num _item_description.description ; Insertion code in PDB sequence ; _item.name '_struct_ref_seq_dif.pdbx_auth_seq_num' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq_dif.ndb_auth_seq_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq_dif.pdbx_seq_db_name _item_description.description ; Sequence database name. ; _item.name '_struct_ref_seq_dif.pdbx_seq_db_name' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code code _item_examples.case 'SWS' _item_aliases.alias_name '_struct_ref_seq_dif.ndb_seq_db_name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq_dif.pdbx_seq_db_accession_code _item_description.description ; Sequence database accession number. ; _item.name '_struct_ref_seq_dif.pdbx_seq_db_accession_code' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code code _item_examples.case 'P07617' _item_aliases.alias_name '_struct_ref_seq_dif.ndb_seq_db_accession_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq_dif.pdbx_seq_db_seq_num _item_description.description ; Sequence database sequence number. ; _item.name '_struct_ref_seq_dif.pdbx_seq_db_seq_num' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code code _item_examples.case '142' _item_aliases.alias_name '_struct_ref_seq_dif.ndb_seq_db_seq_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_sheet_range.pdbx_beg_PDB_ins_code _item_description.description ; A component of the identifier for the residue at which the beta sheet range begins. Insertion code. ; _item.name '_struct_sheet_range.pdbx_beg_PDB_ins_code' _item.category_id struct_sheet_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_range.pdbx_beg_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_sheet_range.ndb_beg_label_ins_code_pdb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_range.pdbx_end_PDB_ins_code _item_description.description ; A component of the identifier for the residue at which the beta sheet range ends. Insertion code. ; _item.name '_struct_sheet_range.pdbx_end_PDB_ins_code' _item.category_id struct_sheet_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_range.pdbx_end_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_sheet_range.ndb_end_label_ins_code_pdb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id _item_description.description ; Pointer to _atom_site.auth_comp_id ; _item.name '_struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_auth_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id _item_description.description ; Pointer to _atom_site.auth_asym_id. ; _item.name '_struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_auth_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_end_auth_comp_id _item_description.description ; Pointer to _atom_site.auth_comp_id. ; _item.name '_struct_sheet_hbond.pdbx_range_1_end_auth_comp_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_auth_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_end_auth_asym_id _item_description.description ; Pointer to _atom_site.auth_comp_id. ; _item.name '_struct_sheet_hbond.pdbx_range_1_end_auth_asym_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_auth_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_beg_label_comp_id _item_description.description ; Pointer to _atom_site.label_comp_id ; _item.name '_struct_sheet_hbond.pdbx_range_1_beg_label_comp_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_beg_label_asym_id _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_struct_sheet_hbond.pdbx_range_1_beg_label_asym_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_end_label_comp_id _item_description.description ; Pointer to _atom_site.label_comp_id. ; _item.name '_struct_sheet_hbond.pdbx_range_1_end_label_comp_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_end_label_asym_id _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_struct_sheet_hbond.pdbx_range_1_end_label_asym_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_2_beg_label_comp_id _item_description.description ; Pointer to _atom_site.label_comp_id. ; _item.name '_struct_sheet_hbond.pdbx_range_2_beg_label_comp_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_beg_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_2_beg_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_2_beg_label_asym_id _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_struct_sheet_hbond.pdbx_range_2_beg_label_asym_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_beg_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_2_beg_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code _item_description.description ; Pointer to _atom_site.pdbx_PDB_ins_code. ; _item.name '_struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_2_beg_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_2_end_label_comp_id _item_description.description ; Pointer to _atom_site.label_comp_id. ; _item.name '_struct_sheet_hbond.pdbx_range_2_end_label_comp_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_end_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_2_end_label_comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_2_end_label_asym_id _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_struct_sheet_hbond.pdbx_range_2_end_label_asym_id' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_end_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_2_end_label_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_sheet_hbond.pdbx_range_2_end_label_ins_code _item_description.description ; Place holder for PDB insertion code. ; _item.name '_struct_sheet_hbond.pdbx_range_2_end_label_ins_code' _item.category_id struct_sheet_hbond _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_struct_sheet_hbond.ndb_range_2_end_label_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## ## save__struct_site.pdbx_num_residues _item_description.description ; Number of residues in the site. ; _item.name '_struct_site.pdbx_num_residues' _item.category_id struct_site _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_struct_site.rcsb_num_residues' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_site_gen.pdbx_auth_ins_code _item_description.description ; PDB insertion code. ; _item.name '_struct_site_gen.pdbx_auth_ins_code' _item.category_id struct_site_gen _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_struct_site_gen.ndb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_site_gen.pdbx_num_res _item_description.description ; Number of residues in the site. ; _item.name '_struct_site_gen.pdbx_num_res' _item.category_id struct_site_gen _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_struct_site_gen.ndb_num_res' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__symmetry.pdbx_full_space_group_name_H-M _item_description.description ; Used for PDB space group: Example: 'C 1 2 1' (instead of C 2) 'P 1 2 1' (instead of P 2) 'P 1 21 1' (instead of P 21) 'P 1 1 21' (instead of P 21 -unique C axis) 'H 3' (instead of R 3 -hexagonal) 'H 3 2' (instead of R 3 2 -hexagonal) ; _item.name '_symmetry.pdbx_full_space_group_name_H-M' _item.category_id symmetry _item.mandatory_code no _item_type.code line _item_examples.case ; Example: 'C 1 2 1' (instead of C 2) 'P 1 2 1' (instead of P 2) 'P 1 21 1' (instead of P 21) 'P 1 1 21' (instead of P 21 -unique C axis) 'H 3' (instead of R 3 -hexagonal) 'H 3 2' (instead of R 3 2 -hexagonal) ; _item_aliases.alias_name '_symmetry.ndb_full_space_group_name_H-M' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save__refine.pdbx_overall_ESU_R _item_description.description ; Overall estimated standard uncertainties of positional parameters based on R value. ; _item.name '_refine.pdbx_overall_ESU_R' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_ESU_R' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_type.code float save_ save__refine.pdbx_overall_ESU_R_Free _item_description.description ; Overall estimated standard uncertainties of positional parameters based on R value. ; _item.name '_refine.pdbx_overall_ESU_R_Free' _item.category_id refine _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_refine.rcsb_overall_ESU_R_Free' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### save_pdbx_refine_tls _category.description ; Data items in the REFINE_TLS category record details about TLS parameters used in structure refinement. Note that the intention is primarily to describe directly refined TLS parameters, although other methods of obtaining TLS parameters may be covered, see item _pdbx_refine_tls.method ; _category.id pdbx_refine_tls _category.mandatory_code no loop_ _category_key.name '_pdbx_refine_tls.id' loop_ _category_group.id 'inclusive_group' 'refine_group' 'ccp4_group' save_ save__pdbx_refine_tls.id _item_description.description ; The value of _pdbx_refine_tls.id must uniquely identify a record in the PDBX_REFINE_TLS list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_pdbx_refine_tls.id' _item.category_id pdbx_refine_tls _item.mandatory_code yes loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.refine_tls_id' '_pdbx_refine_tls.id' _item_type.code code loop_ _item_examples.case 1 A loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.details _item_description.description ; A description of the TLS group, such as a domain name or a chemical group name. ; _item.name '_pdbx_refine_tls.details' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Chain A catalytic domain' 'Chain A Tyr 56 side chain' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.details' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.details' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.method _item_description.description ; The method by which the TLS parameters were obtained. ; _item.name '_pdbx_refine_tls.method' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail refined ; TLS parameters refined directly against crystallographic residual ; fitted ; TLS parameters fitted to previously refined anisotropic displacement parameters ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.method' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.method' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.origin_x _item_description.description ; The x coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in _atom_sites.Cartn_transform_axes. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.origin_x' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_dependent.dependent_name '_pdbx_refine_tls.origin_y' '_pdbx_refine_tls.origin_z' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.origin_x' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.origin_x' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.origin_y _item_description.description ; The y coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in _atom_sites.Cartn_transform_axes. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.origin_y' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_dependent.dependent_name '_pdbx_refine_tls.origin_x' '_pdbx_refine_tls.origin_z' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.origin_y' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.origin_y' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.origin_z _item_description.description ; The z coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in _atom_sites.Cartn_transform_axes. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.origin_z' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_dependent.dependent_name '_pdbx_refine_tls.origin_x' '_pdbx_refine_tls.origin_y' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.origin_z' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.origin_z' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[1][1] _item_description.description ; The [1][1] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.T[1][1]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[1][1]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[1][1]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[1][1]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[1][1]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.T[1][1]. ; _item.name '_pdbx_refine_tls.T[1][1]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[1][1]' associated_value _item_units.code angstroms_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[1][1]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[1][1]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[1][2] _item_description.description ; The [1][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.T[1][2]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[1][2]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[1][2]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[1][2]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[1][2]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.T[1][2]. ; _item.name '_pdbx_refine_tls.T[1][2]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[1][2]' associated_value _item_units.code angstroms_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[1][2]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[1][2]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[1][3] _item_description.description ; The [1][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.T[1][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[1][3]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[1][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[1][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[1][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.T[1][3]. ; _item.name '_pdbx_refine_tls.T[1][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[1][3]' associated_value _item_units.code angstroms_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[1][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[1][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[2][2] _item_description.description ; The [2][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.T[2][2]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[2][2]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[2][2]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[2][2]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[2][2]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.T[2][2]. ; _item.name '_pdbx_refine_tls.T[2][2]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[2][2]' associated_value _item_units.code angstroms_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[2][2]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[2][2]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[2][3] _item_description.description ; The [2][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.T[2][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[2][3]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[2][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[2][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[2][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.T[2][3]. ; _item.name '_pdbx_refine_tls.T[2][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[2][3]' associated_value _item_units.code angstroms_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[2][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[2][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[3][3] _item_description.description ; The [3][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.T[3][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[3][3]_esd' associated_esd _item_units.code angstroms_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[3][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[3][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.T[3][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.T[3][3]. ; _item.name '_pdbx_refine_tls.T[3][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.T[3][3]' associated_value _item_units.code angstroms_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.T[3][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.T[3][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[1][1] _item_description.description ; The [1][1] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.L[1][1]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[1][1]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[1][1]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[1][1]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[1][1]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.L[1][1]. ; _item.name '_pdbx_refine_tls.L[1][1]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[1][1]' associated_value _item_units.code degrees_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[1][1]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[1][1]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[1][2] _item_description.description ; The [1][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.L[1][2]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[1][2]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[1][2]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[1][2]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[1][2]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.L[1][2]. ; _item.name '_pdbx_refine_tls.L[1][2]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[1][2]' associated_value _item_units.code degrees_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[1][2]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[1][2]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[1][3] _item_description.description ; The [1][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.L[1][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[1][3]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[1][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[1][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[1][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.L[1][3]. ; _item.name '_pdbx_refine_tls.L[1][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[1][3]' associated_value _item_units.code degrees_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[1][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[1][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[2][2] _item_description.description ; The [2][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.L[2][2]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[2][2]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[2][2]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[2][2]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[2][2]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.L[2][2]. ; _item.name '_pdbx_refine_tls.L[2][2]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[2][2]' associated_value _item_units.code degrees_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[2][2]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[2][2]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[2][3] _item_description.description ; The [2][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.L[2][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[2][3]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[2][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[2][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[2][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.L[2][3]. ; _item.name '_pdbx_refine_tls.L[2][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[2][3]' associated_value _item_units.code degrees_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[2][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[2][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[3][3] _item_description.description ; The [3][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. ; _item.name '_pdbx_refine_tls.L[3][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[3][3]_esd' associated_esd _item_units.code degrees_squared _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[3][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[3][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.L[3][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.L[3][3]. ; _item.name '_pdbx_refine_tls.L[3][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.L[3][3]' associated_value _item_units.code degrees_squared loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.L[3][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.L[3][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[1][1] _item_description.description ; The [1][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. ; _item.name '_pdbx_refine_tls.S[1][1]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[1][1]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[1][1]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[1][1]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[1][1]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[1][1]. ; _item.name '_pdbx_refine_tls.S[1][1]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[1][1]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[1][1]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[1][1]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[1][2] _item_description.description ; The [1][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.S[1][2]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[1][2]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[1][2]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[1][2]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[1][2]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[1][2]. ; _item.name '_pdbx_refine_tls.S[1][2]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[1][2]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[1][2]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[1][2]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[1][3] _item_description.description ; The [1][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.S[1][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[1][3]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[1][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[1][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[1][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[1][3]. ; _item.name '_pdbx_refine_tls.S[1][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[1][3]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[1][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[1][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[2][1] _item_description.description ; The [2][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.S[2][1]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[2][1]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[2][1]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[2][1]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[2][1]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[2][1]. ; _item.name '_pdbx_refine_tls.S[2][1]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[2][1]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[2][1]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[2][1]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[2][2] _item_description.description ; The [2][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. ; _item.name '_pdbx_refine_tls.S[2][2]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[2][2]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[2][2]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[2][2]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[2][2]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[2][2]. ; _item.name '_pdbx_refine_tls.S[2][2]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[2][2]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[2][2]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[2][2]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[2][3] _item_description.description ; The [2][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.S[2][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[2][3]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[2][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[2][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[2][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[2][3]. ; _item.name '_pdbx_refine_tls.S[2][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[2][3]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[2][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[2][3]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[3][1] _item_description.description ; The [3][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.S[3][1]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[3][1]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[3][1]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[3][1]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[3][1]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[3][1]. ; _item.name '_pdbx_refine_tls.S[3][1]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[3][1]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[3][1]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[3][1]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[3][2] _item_description.description ; The [3][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric ; _item.name '_pdbx_refine_tls.S[3][2]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[3][2]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[3][2]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[3][2]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[3][2]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[3][2]. ; _item.name '_pdbx_refine_tls.S[3][2]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[3][2]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[3][2]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[3][2]_esd' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[3][3] _item_description.description ; The [3][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. ; _item.name '_pdbx_refine_tls.S[3][3]' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[3][3]_esd' associated_esd _item_units.code angstroms_degrees _item_type_conditions.code esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[3][3]' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[3][3]' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls.S[3][3]_esd _item_description.description ; The estimated standard deviation of _pdbx_refine_tls.S[3][3]. ; _item.name '_pdbx_refine_tls.S[3][3]_esd' _item.category_id pdbx_refine_tls _item.mandatory_code no _item_type.code float _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_pdbx_refine_tls.S[3][3]' associated_value _item_units.code angstroms_degrees loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls.S[3][3]_esd' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls.S[3][3]_esd' 'cif_ccp4.dic' 1.0 save_ save_pdbx_refine_tls_group _category.description ; Data items in the PDBX_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in PDBX_REFINE_TLS ; _category.id pdbx_refine_tls_group _category.mandatory_code no loop_ _category_key.name '_pdbx_refine_tls_group.id' loop_ _category_group.id 'inclusive_group' 'refine_group' 'ccp4_group' save_ save__pdbx_refine_tls_group.id _item_description.description ; The value of _pdbx_refine_tls_group.id must uniquely identify a record in the REFINE_TLS_GROUP list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_pdbx_refine_tls_group.id' _item.category_id pdbx_refine_tls_group _item.mandatory_code yes _item_type.code code loop_ _item_examples.case 1 A loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.refine_tls_id _item_description.description ; This data item is a pointer to _pdbx_refine_tls.id in the REFINE_TLS category. ; _item.name '_pdbx_refine_tls_group.refine_tls_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.refine_tls_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.refine_tls_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.beg_label_asym_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.beg_label_asym_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.beg_label_asym_id' '_atom_site.label_asym_id' loop_ _item_examples.case O 2B3 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.beg_label_asym_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.beg_label_asym_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.beg_label_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.beg_label_seq_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.beg_label_seq_id' '_atom_site.label_seq_id' loop_ _item_examples.case 1 303 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.beg_label_seq_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.beg_label_seq_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.beg_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.beg_auth_asym_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.beg_auth_asym_id' '_atom_site.auth_asym_id' loop_ _item_examples.case O 2B3 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.beg_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.beg_auth_seq_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.beg_auth_seq_id' '_atom_site.auth_seq_id' loop_ _item_examples.case 1 5A loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.end_label_asym_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.end_label_asym_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.end_label_asym_id' '_atom_site.label_asym_id' loop_ _item_examples.case O 2B3 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.end_label_asym_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.end_label_asym_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.end_label_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.end_label_seq_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.end_label_seq_id' '_atom_site.label_seq_id' loop_ _item_examples.case 1 303 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.end_label_seq_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.end_label_seq_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.end_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.end_auth_asym_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.end_auth_asym_id' '_atom_site.auth_asym_id' loop_ _item_examples.case O 2B3 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.end_auth_asym_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.end_auth_asym_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.end_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_refine_tls_group.end_auth_seq_id' _item.category_id pdbx_refine_tls_group _item.mandatory_code no loop_ _item_linked.child_name _item_linked.parent_name '_pdbx_refine_tls_group.end_auth_seq_id' '_atom_site.auth_seq_id' loop_ _item_examples.case 1 5A loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.end_auth_seq_id' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.end_auth_seq_id' 'cif_ccp4.dic' 1.0 save_ save__pdbx_refine_tls_group.selection _item_description.description ; A description of the subset of atoms in the specified range included in the TLS fragment. ; _item.name '_pdbx_refine_tls_group.selection' _item.category_id pdbx_refine_tls_group _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail all ; all atoms in specified range ; mnc ; main chain atoms only ; sdc ; side chain atoms only ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_ccp4_refine_tls_group.selection' 'cif_rcsb.dic' 1.1 '_ccp4_refine_tls_group.selection' 'cif_ccp4.dic' 1.0 save_ # save__refine.pdbx_solvent_vdw_probe_radii _item_description.description ; CCP4 solvent proble van der Waals radii ; _item.name '_refine.pdbx_solvent_vdw_probe_radii' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine.ccp4_solvent_vdw_probe_radii' 'cif_rcsb.dic' 1.1 '_refine.ccp4_solvent_vdw_probe_radii' 'cif_ccp4.dic' 1.0 save_ save__refine.pdbx_solvent_ion_probe_radii _item_description.description ; CCP4 solvent ion proble radii ; _item.name '_refine.pdbx_solvent_ion_probe_radii' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine.ccp4_solvent_ion_probe_radii' 'cif_rcsb.dic' 1.1 '_refine.ccp4_solvent_ion_probe_radii' 'cif_ccp4.dic' 1.0 save_ save__refine.pdbx_solvent_shrinkage_radii _item_description.description ; CCP4 solvent shrinkage radii ; _item.name '_refine.pdbx_solvent_shrinkage_radii' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine.ccp4_solvent_shrinkage_radii' 'cif_rcsb.dic' 1.1 '_refine.ccp4_solvent_shrinkage_radii' 'cif_ccp4.dic' 1.0 save_ ######################### ## PDBX_CONTACT_AUTHOR ## ######################### save_pdbx_contact_author _category.description ; Data items in the PDBX_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. This category atomizes information to a greater degree than the standard AUDIT_CONTACT_AUTHOR category. ; _category.id pdbx_contact_author _category.mandatory_code no _category_key.name '_pdbx_contact_author.id' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _pdbx_contact_author.id 1 _pdbx_contact_author.name_salutation 'Dr.' _pdbx_contact_author.name_first 'Paula' _pdbx_contact_author.name_last 'Fitzgerald' _pdbx_contact_author.name_mi 'M.D.' _pdbx_contact_author.address_1 'Department of Biophysical Chemistry' _pdbx_contact_author.address_2 'Merck Research Laboratories' _pdbx_contact_author.address_3 'P. O. Box 2000, Ry80M203' _pdbx_contact_author.city 'Rahway' _pdbx_contact_author.state_province 'New Jersey' _pdbx_contact_author.postal_code 07065 _pdbx_contact_author.country 'UNITED STATES' _pdbx_contact_author.phone '908 594 5510' _pdbx_contact_author.fax '908 594 6645' _pdbx_contact_author.email 'paula_fitzgerald@merck.com' _pdbx_contact_author.role 'principal investigator' _pdbx_contact_author.organization_type 'commercial' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_contact_author.id _item_description.description ; A unique integer identifier for this author ; _item.name '_pdbx_contact_author.id' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code int _item_examples.case ; 1 2 3 ; loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 save_ save__pdbx_contact_author.address_1 _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed, line 1 of 3. ; _item.name '_pdbx_contact_author.address_1' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code text _item_examples.case ; 610 Taylor Road ; save_ save__pdbx_contact_author.address_2 _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed, line 2 of 3. ; _item.name '_pdbx_contact_author.address_2' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code text _item_examples.case ; Department of Chemistry and Chemical Biology ; save_ save__pdbx_contact_author.address_3 _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed, line 3 of 3. ; _item.name '_pdbx_contact_author.address_3' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code text _item_examples.case ; Busch Campus ; save_ save__pdbx_contact_author.city _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed, city. ; _item.name '_pdbx_contact_author.city' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line _item_examples.case ; Piscataway ; save_ save__pdbx_contact_author.state_province _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed, state or province. ; _item.name '_pdbx_contact_author.state_province' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line _item_examples.case ; New Jersey ; save_ save__pdbx_contact_author.postal_code _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed, zip code. ; _item.name '_pdbx_contact_author.postal_code' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line _item_examples.case ; 08854 ; save_ save__pdbx_contact_author.email _item_description.description ; The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognisable to international networks. ; _item.name '_pdbx_contact_author.email' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'name@host.domain.country' 'bm@iucr.ac.uk' save_ save__pdbx_contact_author.fax _item_description.description ; The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number with no spaces. ; _item.name '_pdbx_contact_author.fax' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line loop_ _item_examples.case '12(34) 947 7334' '732 445 0103' save_ save__pdbx_contact_author.name_first _item_description.description ; The first name of the author of the data block to whom correspondence should be addressed. ; _item.name '_pdbx_contact_author.name_first' _item.category_id pdbx_contact_author _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Percival' 'Loyd' 'Susan' save_ save__pdbx_contact_author.name_last _item_description.description ; The last name of the author of the data block to whom correspondence should be addressed. ; _item.name '_pdbx_contact_author.name_last' _item.category_id pdbx_contact_author _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Samuels' 'Rodgers' save_ save__pdbx_contact_author.name_mi _item_description.description ; The middle initial(s) of the author of the data block to whom correspondence should be addressed. ; _item.name '_pdbx_contact_author.name_mi' _item.category_id pdbx_contact_author _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'T.' 'M.F.' save_ save__pdbx_contact_author.name_salutation _item_description.description ; The salutation of the author of the data block to whom correspondence should be addressed. ; _item.name '_pdbx_contact_author.name_salutation' _item.category_id pdbx_contact_author _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Dr.' 'Prof.' 'Mr.' 'Ms.' 'Mrs.' loop_ _item_enumeration.value 'Dr.' 'Prof.' 'Mr.' 'Ms.' 'Mrs.' save_ save__pdbx_contact_author.country _item_description.description ; The country of the author of the data block to whom correspondence should be addressed. ; _item.name '_pdbx_contact_author.country' _item.category_id pdbx_contact_author _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'UNITED STATES' 'UNITED KINGDOM' 'AUSTRALIA' loop_ _item_enumeration.value 'UNITED STATES' 'AFGHANISTAN' 'ALBANIA' 'ALGERIA' 'AMERICAN SAMOA' 'ANDORRA' 'ANGOLA' 'ANGUILLA' 'ANTARCTICA' 'ANTIGUA AND BARBUDA' 'ARGENTINA' 'ARMENIA' 'ARUBA' 'AUSTRALIA' 'AUSTRIA' 'AZERBAIJAN' 'BAHAMAS' 'BAHRAIN' 'BANGLADESH' 'BARBADOS' 'BELARUS' 'BELGIUM' 'BELIZE' 'BENIN' 'BERMUDA' 'BHUTAN' 'BOLIVIA' 'BOSNIA AND HERZEGOVINA' 'BOTSWANA' 'BOUVET ISLAND' 'BRAZIL' 'BRITISH INDIAN OCEAN TERRITORY' 'BRUNEI DARUSSALAM' 'BULGARIA' 'BURKINA FASO' 'BURUNDI' 'CAMBODIA' 'CAMEROON' 'CANADA' 'CAPE VERDE' 'CAYMAN ISLANDS' 'CENTRAL AFRICAN REPUBLIC' 'CHAD' 'CHILE' 'CHINA' 'CHRISTMAS ISLAND' 'COCOS (KEELING) ISLANDS' 'COLOMBIA' 'COMOROS' 'CONGO' 'CONGO, THE DEMOCRATIC REPUBLIC OF THE' 'COOK ISLANDS' 'COSTA RICA' 'COTE D'IVOIRE' 'CROATIA' 'CUBA' 'CYPRUS' 'CZECH REPUBLIC' 'DENMARK' 'DJIBOUTI' 'DOMINICA' 'DOMINICAN REPUBLIC' v'ECUADOR' 'EGYPT' 'EL SALVADOR' 'EQUATORIAL GUINEA' 'ERITREA' 'ESTONIA' 'ETHIOPIA' 'FALKLAND ISLANDS (MALVINAS)' 'FAROE ISLANDS' 'FIJI' 'FINLAND' 'FRANCE' 'FRENCH GUIANA' 'FRENCH POLYNESIA' 'FRENCH SOUTHERN TERRITORIES' 'GABON' 'GAMBIA' 'GEORGIA' 'GERMANY' 'GHANA' 'GIBRALTAR' 'GREECE' 'GREENLAND' 'GRENADA' 'GUADELOUPE' 'GUAM' 'GUATEMALA' 'GUINEA' 'GUINEA-BISSAU' 'GUYANA' 'HAITI' 'HEARD ISLAND AND MCDONALD ISLANDS' 'HOLY SEE (VATICAN CITY STATE)' 'HONDURAS' 'HONG KONG' 'HUNGARY' 'ICELAND' 'INDIA' 'INDONESIA' 'IRAN, ISLAMIC REPUBLIC OF' 'IRAQ' 'IRELAND' 'ISRAEL' 'ITALY' 'JAMAICA' 'JAPAN' 'JORDAN' 'KAZAKHSTAN' 'KENYA' 'KIRIBATI' 'KOREA, DEMOCRATIC PEOPLE'S REPUBLIC OF' 'KOREA, REPUBLIC OF' 'KUWAIT' 'KYRGYZSTAN' 'LAO PEOPLE'S DEMOCRATIC REPUBLIC' 'LATVIA' 'LEBANON' 'LESOTHO' 'LIBERIA' 'LIBYAN ARAB JAMAHIRIYA' 'LIECHTENSTEIN' 'LITHUANIA' 'LUXEMBOURG' 'MACAO' 'MACEDONIA, THE FORMER YUGOSLAV REPUBLIC OF' 'MADAGASCAR' 'MALAWI' 'MALAYSIA' 'MALDIVES' 'MALI' 'MALTA' 'MARSHALL ISLANDS' 'MARTINIQUE' 'MAURITANIA' 'MAURITIUS' 'MAYOTTE' 'MEXICO' 'MICRONESIA, FEDERATED STATES OF' 'MOLDOVA, REPUBLIC OF' 'MONACO' 'MONGOLIA' 'MONTSERRAT' 'MOROCCO' 'MOZAMBIQUE' 'MYANMAR' 'NAMIBIA' 'NAURU' 'NEPAL' 'NETHERLANDS' 'NETHERLANDS ANTILLES' 'NEW CALEDONIA' 'NEW ZEALAND' 'NICARAGUA' 'NIGER' 'NIGERIA' 'NIUE' 'NORFOLK ISLAND' 'NORTHERN MARIANA ISLANDS' 'NORWAY' 'OMAN' 'PAKISTAN' 'PALAU' 'PALESTINIAN TERRITORY, OCCUPIED' 'PANAMA' 'PAPUA NEW GUINEA' 'PARAGUAY' 'PERU' 'PHILIPPINES' 'PITCAIRN' 'POLAND' 'PORTUGAL' 'PUERTO RICO' 'QATAR' 'REUNION' 'ROMANIA' 'RUSSIAN FEDERATION' 'RWANDA' 'SAINT HELENA' 'SAINT KITTS AND NEVIS' 'SAINT LUCIA' 'SAINT PIERRE AND MIQUELON' 'SAINT VINCENT AND THE GRENADINES' 'SAMOA' 'SAN MARINO' 'SAO TOME AND PRINCIPE' 'SAUDI ARABIA' 'SENEGAL' 'SERBIA AND MONTENEGRO' 'SEYCHELLES' 'SIERRA LEONE' 'SINGAPORE' 'SLOVAKIA' 'SLOVENIA' 'SOLOMON ISLANDS' 'SOMALIA' 'SOUTH AFRICA' 'SOUTH GEORGIA AND THE SOUTH SANDWICH ISLANDS' 'SPAIN' 'SRI LANKA' 'SUDAN' 'SURINAME' 'SVALBARD AND JAN MAYEN' 'SWAZILAND' 'SWEDEN' 'SWITZERLAND' 'SYRIAN ARAB REPUBLIC' 'TAIWAN, PROVINCE OF CHINA' 'TAJIKISTAN' 'TANZANIA, UNITED REPUBLIC OF' 'THAILAND' 'TIMOR-LESTE' 'TOGO' 'TOKELAU' 'TONGA' 'TRINIDAD AND TOBAGO' 'TUNISIA' 'TURKEY' 'TURKMENISTAN' 'TURKS AND CAICOS ISLANDS' 'TUVALU' 'UGANDA' 'UKRAINE' 'UNITED ARAB EMIRATES' 'UNITED KINGDOM' 'UNITED STATES MINOR OUTLYING ISLANDS' 'URUGUAY' 'UZBEKISTAN' 'VANUATU' 'VENEZUELA' 'VIET NAM' 'VIRGIN ISLANDS, BRITISH' 'VIRGIN ISLANDS, U.S.' 'WALLIS AND FUTUNA' 'WESTERN SAHARA' 'YEMEN' 'ZAMBIA' 'ZIMBABWE' save_ save__pdbx_contact_author.phone _item_description.description ; The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. ; _item.name '_pdbx_contact_author.phone' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line loop_ _item_examples.case '12 (34) 947 7330' '947 732 0103 x8320' save_ save__pdbx_contact_author.role _item_description.description ; The role of this author in the project depositing this data. ; _item.name '_pdbx_contact_author.role' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'principal investigator' 'responsible scientist' 'investigator' loop_ _item_enumeration.value 'principal investigator' 'responsible scientist' 'investigator' save_ save__pdbx_contact_author.organization_type _item_description.description ; The organization type to which this author is affiliated. ; _item.name '_pdbx_contact_author.organization_type' _item.category_id pdbx_contact_author _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'academic' 'commercial' 'government' 'other' loop_ _item_enumeration.value 'academic' 'commercial' 'government' 'other' save_ save__struct_ref_seq_dif.pdbx_ordinal _item_description.description ; A synthetic integer primary key for this category. ; _item.name '_struct_ref_seq_dif.pdbx_ordinal' _item.category_id struct_ref_seq_dif _item.mandatory_code yes _item_type.code int _item_aliases.alias_name '_struct_ref_seq_dif.rcsb_ordinal' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ##################### ## PDBX_SG_PROJECT ## ##################### save_pdbx_SG_project _category.description ; Data items in the PDBX_CONTACT_AUTHOR category record details about the Structural Genomics Project and name and initials for each Center. ; _category.id pdbx_SG_project _category.mandatory_code no _category_key.name '_pdbx_SG_project.id' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Berkeley Structural Genomics Center' _pdbx_SG_project.initial_of_center BSGC ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_SG_project.id _item_description.description ; A unique integer identifier for this center ; _item.name '_pdbx_SG_project.id' _item.category_id pdbx_SG_project _item.mandatory_code yes _item_type.code int _item_examples.case ; 1 2 3 ; loop_ _item_enumeration.value 1 2 3 4 5 6 7 8 9 10 save_ save__pdbx_SG_project.project_name _item_description.description ; The value identifies the Structural Genomics project. ; _item.name '_pdbx_SG_project.project_name' _item.category_id pdbx_SG_project _item.mandatory_code no _item_type.code text _item_examples.case 'PSI, Protein Structure Initiative' loop_ _item_enumeration.value 'PSI, Protein Structure Initiative' 'NPPSFA, National Project on Protein Structural and Functional Analyses' save_ save__pdbx_SG_project.full_name_of_center _item_description.description ; The value identifies the full name of center. ; _item.name '_pdbx_SG_project.full_name_of_center' _item.category_id pdbx_SG_project _item.mandatory_code no _item_type.code text _item_examples.case 'Berkeley Structural Genomics Center' loop_ _item_enumeration.value 'Bacterial targets at IGS-CNRS France' 'Berkeley Structural Genomics Center' 'Center for Eukaryotic Structural Genomics' 'Israel Structural Proteomics Center' 'Joint Center for Structural Genomics' 'Marseilles Structural Genomics Program @ AFMB' 'Midwest Center for Structural Genomics' 'Montreal-Kingston Bacterial Structural Genomics Initiative' 'Mycobacterium Tuberculosis Structural Proteomics Project' 'New York Structural Genomics Research Consortium' 'Northeast Structural Genomics Consortium' 'Oxford Protein Production Facility' 'Paris-Sud Yeast Structural Genomics' 'Protein Structure Factory' 'RIKEN Structural Genomics/Proteomics Initiative' 'Southeast Collaboratory for Structural Genomics' 'Structural Genomics Consortium' 'Structural Genomics of Pathogenic Protozoa Consortium' 'Structural Proteomics in Europe' 'Structure 2 Function Project' 'TB Structural Genomics Consortium' save_ save__pdbx_SG_project.initial_of_center _item_description.description ; The value identifies the full name of center. ; _item.name '_pdbx_SG_project.initial_of_center' _item.category_id pdbx_SG_project _item.mandatory_code no _item_type.code text _item_examples.case 'BSGC' loop_ _item_enumeration.value 'BIGS' 'BSGC' 'CESG' 'ISPC' 'JCSG' 'MSGP' 'MCSG' 'BSGI' 'XMTB' 'NYSGRC' 'NESG' 'OPPF' 'YSG' 'PSF' 'RSGI' 'SECSG' 'SGC' 'SGPP' 'SPINE' 'S2F' 'TBSGC' save_ ### EOF mmcif_pdbx-def-1.dic ########################################################################### # # File: mmcif_pdbx-def-3.dic # # PDB Exchange Data Dictionary # # This data dictionary contains definitions used by wwPDB for data exchange # and data processing. # # Definition Section 3 # # ########################################################################### ## ## save_pdbx_nmr_details _category.description ; Experimental details of the NMR study that have not been described elsewhere in this deposition. ; _category.id pdbx_nmr_details _category.mandatory_code no loop_ _category_key.name '_pdbx_nmr_details.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' save_ save__pdbx_nmr_details.entry_id _item_description.description ; The entry ID for the structure determination. ; _item.name '_pdbx_nmr_details.entry_id' _item.category_id pdbx_nmr_details _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nmr_details.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_rcsb_nmr_details.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_details.text _item_description.description ; Additional details describing the NMR experiment. ; _item.name '_pdbx_nmr_details.text' _item.category_id pdbx_nmr_details _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; This structure was determined using standard 2D homonuclear techniques. ; ; The structure was determined using triple-resonance NMR spectroscopy. ; _item_aliases.alias_name '_rcsb_nmr_details.text' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## ## provided to hold a simple solution description. save_pdbx_nmr_sample_details _category.description ; Complete description of each NMR sample, including the solvent system used. ; _category.id pdbx_nmr_sample_details _category.mandatory_code no loop_ _category_key.name '_pdbx_nmr_sample_details.solution_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. ; ; loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.contents 1 MCP-1 '2 mM U-15N,13C, H2O 90 %, D2O 10 %' 2 MCP-1 '1 mM U-50% 15N, MCP-1 1 mM U-50% 13C, H2O 90 %, D2O 10 %' 3 MCP-1 '2 mM U-15N, H2O 90 %, D2O 10 %' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_sample_details.solution_id _item_description.description ; The name (number) of the sample. ; _item.name '_pdbx_nmr_sample_details.solution_id' _item.category_id pdbx_nmr_sample_details _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' '3' _item_aliases.alias_name '_rcsb_nmr_sample_details.solution_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_sample_details.contents _item_description.description ; A complete description of each NMR sample. Include the concentration and concentration units for each component (include buffers, etc.). For each component describe the isotopic composition, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labeled biomolecule is designated by NA: U-13C; NA-K,H ; _item.name '_pdbx_nmr_sample_details.contents' _item.category_id pdbx_nmr_sample_details _item.mandatory_code no _item_type.code text _item_examples.case ; 2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O ; _item_aliases.alias_name '_rcsb_nmr_sample_details.contents' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_sample_details.solvent_system _item_description.description ; The solvent system used for this sample. ; _item.name '_pdbx_nmr_sample_details.solvent_system' _item.category_id pdbx_nmr_sample_details _item.mandatory_code no _item_type.code text _item_examples.case ; 90% H2O, 10% D2O ; _item_aliases.alias_name '_rcsb_nmr_sample_details.solvent_system' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save_pdbx_nmr_exptl_sample _category.description ; The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name. ; _category.id pdbx_nmr_exptl_sample _category.mandatory_code no loop_ _category_key.name '_pdbx_nmr_exptl_sample.solution_id' '_pdbx_nmr_exptl_sample.component' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. ; # ; loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 MCP-1 2 'mM' 'U-15N,13C' 1 H2O 90 '%' . 1 D2O 10 '%' . ; ; Example 2 This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. ; # ; loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 2 MCP-1 1 'mM' 'U-50% 15N' 2 H2O 90 '%' . 2 D2O 10 '%' . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_exptl_sample.solution_id _item_description.description ; The name (number) of the sample. ; _item.name '_pdbx_nmr_exptl_sample.solution_id' _item.category_id pdbx_nmr_exptl_sample _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' '3' _item_aliases.alias_name '_rcsb_nmr_exptl_sample.solution_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample.component _item_description.description ; The name of each component in the sample ; _item.name '_pdbx_nmr_exptl_sample.component' _item.category_id pdbx_nmr_exptl_sample _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'ribonuclease' 'DNA strand 1' 'TRIS buffer' 'sodium chloride' 'H2O' 'D2O' _item_aliases.alias_name '_rcsb_nmr_exptl_sample.component' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample.concentration _item_description.description ; The concentration value of the component. ; _item.name '_pdbx_nmr_exptl_sample.concentration' _item.category_id pdbx_nmr_exptl_sample _item.mandatory_code no _item_type.code float loop_ _item_examples.case '2.0' '2.7' '0.01' _item_aliases.alias_name '_rcsb_nmr_exptl_sample.concentration' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample.concentration_units _item_description.description ; The concentration units of the component. ; _item.name '_pdbx_nmr_exptl_sample.concentration_units' _item.category_id pdbx_nmr_exptl_sample _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'mg/mL for mg per milliliter' 'mM for millimolar' '% for percent by volume' loop_ _item_enumeration.value _item_enumeration.detail '%' 'percent by volume' 'mM' 'millimolar' 'mg/mL' 'mg per milliliter' 'M' 'molar' 'g/L' 'grams per liter' _item_aliases.alias_name '_rcsb_nmr_exptl_sample.concentration_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample.isotopic_labeling _item_description.description ; The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H ; _item.name '_pdbx_nmr_exptl_sample.isotopic_labeling' _item.category_id pdbx_nmr_exptl_sample _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'U-13C,15N' 'U-2H' loop_ _item_enumeration.value 'U-15N' 'U-13C' 'U-15N,13C' 'U-2H' 'other' _item_aliases.alias_name '_rcsb_nmr_exptl_sample.isotopic_labeling' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ########################################################################## ### save_pdbx_nmr_exptl_sample_conditions _category.description ; The experimental conditions used to for each sample. Each set of conditions is identified by a numerical code. ; _category.id pdbx_nmr_exptl_sample_conditions _category.mandatory_code no loop_ _category_key.name '_pdbx_nmr_exptl_sample_conditions.conditions_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example was taken from a pH stability study. ; # ; loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength 1 298 ambient 7 '25mM NaCl' 2 298 ambient 3 '25mM NaCl' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_exptl_sample_conditions.conditions_id _item_description.description ; The condition number as defined above. ; _item.name '_pdbx_nmr_exptl_sample_conditions.conditions_id' _item.category_id pdbx_nmr_exptl_sample_conditions _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' '3' _item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.conditions_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample_conditions.temperature _item_description.description ; The temperature (in Kelvin) at which NMR data were collected. ; _item.name '_pdbx_nmr_exptl_sample_conditions.temperature' _item.category_id pdbx_nmr_exptl_sample_conditions _item.mandatory_code no _item_type.code float-range loop_ _item_examples.case '298' _item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.temperature' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample_conditions.pressure_units _item_description.description ; The units of pressure at which NMR data were collected. ; _item.name '_pdbx_nmr_exptl_sample_conditions.pressure_units' _item.category_id pdbx_nmr_exptl_sample_conditions _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'Pa' 'atm' 'Torr' _item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.pressure_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample_conditions.pressure _item_description.description ; The pressure at which NMR data were collected. ; _item.name '_pdbx_nmr_exptl_sample_conditions.pressure' _item.category_id pdbx_nmr_exptl_sample_conditions _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'ambient' '1atm' _item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.pressure' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample_conditions.pH _item_description.description ; The pH at which the NMR data were collected. ; _item.name '_pdbx_nmr_exptl_sample_conditions.pH' _item.category_id pdbx_nmr_exptl_sample_conditions _item.mandatory_code no _item_type.code float-range loop_ _item_examples.case '3.1' '7.0' _item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.pH' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl_sample_conditions.ionic_strength _item_description.description ; The ionic strength at which the NMR data were collected -in lieu of this enter the concentration and identity of the salt in the sample. ; _item.name '_pdbx_nmr_exptl_sample_conditions.ionic_strength' _item.category_id pdbx_nmr_exptl_sample_conditions _item.mandatory_code no _item_type.code line # loop_ # _item_examples.case # '3.1' # '7.0' _item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.ionic_strength' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ########################################################################## ### save_pdbx_nmr_spectrometer _category.description ; The details about each spectrometer used to collect data for this deposition. ; _category.id pdbx_nmr_spectrometer _category.mandatory_code no _category_key.name '_pdbx_nmr_spectrometer.spectrometer_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; The instruments described here are the ones used for the MCP-1 studies. ; # ; loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.field_strength 1 'Bruker AMX' 600 2 'Bruker AMX' 500 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_spectrometer.spectrometer_id _item_description.description ; Assign a numerical ID to each instrument. ; _item.name '_pdbx_nmr_spectrometer.spectrometer_id' _item.category_id pdbx_nmr_spectrometer _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' '3' _item_aliases.alias_name '_rcsb_nmr_spectrometer.spectrometer_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_spectrometer.model _item_description.description ; The model of the NMR spectrometer. ; _item.name '_pdbx_nmr_spectrometer.model' _item.category_id pdbx_nmr_spectrometer _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'AVANCE' 'WH' 'WM' 'AM' 'AMX' 'DMX' 'DRX' 'MSL' 'OMEGA' 'OMEGA PSG' 'GX' 'GSX' 'A' 'AL' 'EC' 'EX' 'LA' 'ECP' 'VXRS' 'UNITY' 'UNITYPLUS' 'INOVA' _item_aliases.alias_name '_rcsb_nmr_spectrometer.model' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_spectrometer.type _item_description.description ; Select the instrument manufacturer(s) and the model(s) of the NMR(s) used for this work. ; _item.name '_pdbx_nmr_spectrometer.type' _item.category_id pdbx_nmr_spectrometer _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Bruker WH' 'Bruker WM' 'Bruker AM' 'Bruker AMX' 'Bruker DMX' 'Bruker DRX' 'Bruker MSL' 'Bruker AVANCE' 'GE Omega' 'GE Omega PSG' 'JEOL GX' 'JEOL GSX' 'JEOL A' 'JEOL AL' 'JEOL EC' 'JEOL EX' 'JEOL LA' 'JEOL ECP' 'Varian VXRS' 'Varian UNITY' 'Varian UNITYplus' 'Varian INOVA' 'other' _item_aliases.alias_name '_rcsb_nmr_spectrometer.type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_spectrometer.manufacturer _item_description.description ; The name of the manufacturer of the spectrometer. ; _item.name '_pdbx_nmr_spectrometer.manufacturer' _item.category_id pdbx_nmr_spectrometer _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Varian' 'Bruker' 'JEOL' 'GE' _item_aliases.alias_name '_rcsb_nmr_spectrometer.manufacturer' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_spectrometer.field_strength _item_description.description ; Select the field strength for protons in MHz. ; _item.name '_pdbx_nmr_spectrometer.field_strength' _item.category_id pdbx_nmr_spectrometer _item.mandatory_code no _item_type.code float loop_ _item_examples.case '360' '400' '500' '600' '750' '800' '850' '900' '950' '1000' _item_aliases.alias_name '_rcsb_nmr_spectrometer.field_strength' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ########################################################################## ### save_pdbx_nmr_exptl _category.description ; In this section, enter information on those experiments that were used to generate constraint data. For each NMR experiment indicate which sample and which sample conditions were used for the experiment. ; _category.id pdbx_nmr_exptl _category.mandatory_code no loop_ _category_key.name '_pdbx_nmr_exptl.experiment_id' '_pdbx_nmr_exptl.conditions_id' '_pdbx_nmr_exptl.solution_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example was taken from the MCP-1 study. ; # ; loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 3 1 '3D_15N-separated_NOESY' 2 1 1 '3D_13C-separated_NOESY' 3 1 2 '4D_13C/15N-separated_NOESY' 4 1 1 '4D_13C-separated_NOESY' 5 1 1 '3D_15N-separated_ROESY' 6 3 1 '3D_13C-separated_ROESY' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_exptl.experiment_id _item_description.description ; A numerical ID for each experiment. ; _item.name '_pdbx_nmr_exptl.experiment_id' _item.category_id pdbx_nmr_exptl _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' '3' _item_aliases.alias_name '_rcsb_nmr_exptl.experiment_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl.conditions_id _item_description.description ; The number to identify the set of sample conditions. ; _item.name '_pdbx_nmr_exptl.conditions_id' _item.category_id pdbx_nmr_exptl _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' '3' _item_aliases.alias_name '_rcsb_nmr_exptl.conditions_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl.solution_id _item_description.description ; The solution_id from the Experimental Sample to identify the sample that these conditions refer to. [Remember to save the entries here before returning to the Experimental Sample form] ; _item.name '_pdbx_nmr_exptl.solution_id' _item.category_id pdbx_nmr_exptl _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' '2' '3' _item_aliases.alias_name '_rcsb_nmr_exptl.solution_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_exptl.type _item_description.description ; The type of NMR experiment. ; _item.name '_pdbx_nmr_exptl.type' _item.category_id pdbx_nmr_exptl _item.mandatory_code no _item_type.code line loop_ _item_examples.case '2D NOESY' '3D_15N-separated_NOESY' '3D_13C-separated_NOESY' '4D_13C-separated_NOESY' '4D_13C/15N-separated_NOESY' '3D_15N-separated_ROESY' '3D_13C-separated_ROESY' 'HNCA-J' 'HNHA' 'DQF-COSY' 'P-COSY' 'PE-COSY' 'E-COSY' _item_aliases.alias_name '_rcsb_nmr_exptl.type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ########################################################################## ### save_pdbx_nmr_software _category.description ; Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used. ; _category.id pdbx_nmr_software _category.mandatory_code no loop_ _category_key.name '_pdbx_nmr_software.name' '_pdbx_nmr_software.version' '_pdbx_nmr_software.classification' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example describes the software used in the MCP-1 study. ; # ; loop_ _pdbx_nmr_software.name _pdbx_nmr_software.authors _pdbx_nmr_software.version _pdbx_nmr_software.classification UXNMR Bruker 940501.3 'collection' FELIX Hare 1.1 'processing' ANSIG Kraulis 3.0 'data analysis' X-PLOR Brunger 3.8 'structure calculation' X-PLOR Brunger 3.8 'refinement' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_software.classification _item_description.description ; The purpose of the software. ; _item.name '_pdbx_nmr_software.classification' _item.category_id pdbx_nmr_software _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'collection' 'processing' 'data analysis' 'structure solution' 'refinement' 'iterative matrix relaxation' # loop_ # _item_enumeration.value # 'collection' # 'processing' # 'data analysis' # 'structure solution' # 'refinement' # 'iterative matrix relaxation' _item_aliases.alias_name '_rcsb_nmr_software.classification' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_software.name _item_description.description ; The name of the software used for the task. ; _item.name '_pdbx_nmr_software.name' _item.category_id pdbx_nmr_software _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'ANSIG' 'AURELIA' 'AZARA' 'CHARMM' 'CORMA' 'DIANA' 'DYANA' 'DSPACE' 'DISGEO' 'DGII' 'DISMAN' 'DINOSAUR' 'DISCOVER' 'FELIX' 'FT_NMR' 'GROMOS' 'IRMA' 'MARDIGRAS' 'NMRPipe' 'SA' 'UXNMR' 'VNMR' 'X-PLOR' 'XWINNMR' _item_aliases.alias_name '_rcsb_nmr_software.name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_software.version _item_description.description ; The version of the software. ; _item.name '_pdbx_nmr_software.version' _item.category_id pdbx_nmr_software _item.mandatory_code yes _item_type.code line loop_ _item_examples.case '940501.3' '2.1' _item_aliases.alias_name '_rcsb_nmr_software.version' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_software.authors _item_description.description ; The name of the authors of the software used in this procedure. ; _item.name '_pdbx_nmr_software.authors' _item.category_id pdbx_nmr_software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Brunger' 'Guentert' _item_aliases.alias_name '_rcsb_nmr_software.authors' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ########################################################################## ### save_pdbx_nmr_constraints _category.description ; This section provides a tabulation of constraint data. ; _category.id pdbx_nmr_constraints _category.mandatory_code no _category_key.name '_pdbx_nmr_constraints.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example uses the data from the MCP-1 structure determination. Remember this is a dimer so there are intersubunit constraints as well as intrasubunit constraints. ; # ; loop_ _pdbx_nmr_constraints.entry_id _pdbx_nmr_constraints.NOE_constraints_total _pdbx_nmr_constraints.NOE_intraresidue_total_count _pdbx_nmr_constraints.NOE_sequential_total_count _pdbx_nmr_constraints.NOE_medium_range_total_count _pdbx_nmr_constraints.NOE_long_range_total_count _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count 1ABC 4458 1144 272 1004 1356 96 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_constraints.entry_id _item_description.description ; You can leave this blank as an ID will be assigned by the MSD to the constraint file. ; _item.name '_pdbx_nmr_constraints.entry_id' _item.category_id pdbx_nmr_constraints _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nmr_constraints.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_rcsb_nmr_constraints.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_constraints_total _item_description.description ; The total number of all NOE constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NOE_constraints_total' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '4458' _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_constraints_total' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_intraresidue_total_count _item_description.description ; The total number of all intraresidue, [i-j]=0, NOE constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NOE_intraresidue_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '1144' _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_intraresidue_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_interentity_total_count _item_description.description ; The total number of interentity, NOE constraints used in the final structure calculation. This field should only be if system is complex -i.e more than one entity e.g. a dimer or ligand-protein complex ; _item.name '_pdbx_nmr_constraints.NOE_interentity_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '272' _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_interentity_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_sequential_total_count _item_description.description ; The total number of sequential, [i-j]=1, NOE constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NOE_sequential_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '1004' _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_sequential_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_medium_range_total_count _item_description.description ; The total number of medium range 1<[i-j]<=5 NOE constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NOE_medium_range_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '682' _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_medium_range_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_long_range_total_count _item_description.description ; The total number of long range [i-j]>5 NOE constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NOE_long_range_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '1356' _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_long_range_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.protein_phi_angle_constraints_total_count _item_description.description ; The total number of phi angle constraints used in the final structure calculation ; _item.name '_pdbx_nmr_constraints.protein_phi_angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '96' _item_aliases.alias_name '_rcsb_nmr_constraints.protein_phi_angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.protein_psi_angle_constraints_total_count _item_description.description ; The total number of psi angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.protein_psi_angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '0' _item_aliases.alias_name '_rcsb_nmr_constraints.protein_psi_angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.protein_chi_angle_constraints_total_count _item_description.description ; The total number of chi angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.protein_chi_angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '66' _item_aliases.alias_name '_rcsb_nmr_constraints.protein_chi_angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.protein_other_angle_constraints_total_count _item_description.description ; The total number of other angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.protein_other_angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '0' _item_aliases.alias_name '_rcsb_nmr_constraints.protein_other_angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_interproton_distance_evaluation _item_description.description ; Describe the method used to quantify the NOE and ROE values. ; _item.name '_pdbx_nmr_constraints.NOE_interproton_distance_evaluation' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; NOE buildup curves with 50, 75, 150 ms mixing times were analyzed. ; ; Noesy cross peak intensities were classified into three different catagories with distances of 1.8-2.7 A, 1.8-3.5 A, 1.8- 5.0 A for strong, medium and weak NOEs. ; _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_interproton_distance_evaluation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_pseudoatom_corrections _item_description.description ; Describe any corrections made for pseudoatoms ; _item.name '_pdbx_nmr_constraints.NOE_pseudoatom_corrections' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; Pseudo-atoms nomenclature and corrections according to Wuethrich, Billeter, and Braun, J. Mol.Biol.(1983) 169, 949-961. ; ; Pseudoatoms were not used. ; _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_pseudoatom_corrections' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NOE_motional_averaging_correction _item_description.description ;Describe any corrections that were made to the NOE data for motional averaging. ; _item.name '_pdbx_nmr_constraints.NOE_motional_averaging_correction' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Replace with item example text' _item_aliases.alias_name '_rcsb_nmr_constraints.NOE_motional_averaging_correction' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__pdbx_nmr_constraints.hydrogen_bond_constraints_total_count _item_description.description ; The total number of hydrogen bond constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.hydrogen_bond_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '6' _item_aliases.alias_name '_rcsb_nmr_constraints.hydrogen_bond_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.disulfide_bond_constraints_total_count _item_description.description ; The total number of disulfide bond constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.disulfide_bond_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '3' _item_aliases.alias_name '_rcsb_nmr_constraints.disulfide_bond_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count _item_description.description ; The total number of nucleic acid alpha-angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '18' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_alpha-angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_beta-angle_constraints_total_count _item_description.description ; The total number of nucleic acid beta-angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_beta-angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '24' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_beta-angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count _item_description.description ; The total number of nucleic acid gamma-angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '12' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_gamma-angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_delta-angle_constraints_total_count _item_description.description ; The total number of nucleic acid delta-angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_delta-angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '15' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_delta-angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count _item_description.description ; The total number of nucleic acid epsilon-angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '31' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_epsilon-angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_chi-angle_constraints_total_count _item_description.description ; The total number of nucleic acid chi-angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_chi-angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '15' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_chi-angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_other-angle_constraints_total_count _item_description.description ; The total number of nucleic acid other-angle constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_other-angle_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '5' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_other-angle_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count _item_description.description ; The total number of nucleic acid sugar pucker constraints used in the final structure calculation. ; _item.name '_pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count' _item.category_id pdbx_nmr_constraints _item.mandatory_code no _item_type.code int loop_ _item_examples.case '10' _item_aliases.alias_name '_rcsb_nmr_constraints.NA_sugar_pucker_constraints_total_count' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ### ### ########################################################################## ### save_pdbx_nmr_ensemble _category.description ; This category contains the information that describes the ensemble of deposited structures. If only an average structure has been deposited skip this section. ; _category.id pdbx_nmr_ensemble _category.mandatory_code no _category_key.name '_pdbx_nmr_ensemble.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ;This example uses the data from the MCP-1 study. ; # ; loop_ _pdbx_nmr_ensemble.entry_id _pdbx_nmr_ensemble.conformers_calculated_total_number _pdbx_nmr_ensemble.conformers_submitted_total_number _pdbx_nmr_ensemble.conformer_selection_criteria _pdbx_nmr_ensemble.representative_conformer 1ABC 40 20 'structures with the least restraint violations' 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_ensemble.entry_id _item_description.description ; Leave this blank as the ID is provided by the MSD ; _item.name '_pdbx_nmr_ensemble.entry_id' _item.category_id pdbx_nmr_ensemble _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nmr_ensemble.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_rcsb_nmr_ensemble.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.conformers_calculated_total_number _item_description.description ; The total number of conformer (models) that were calculated in the final round. ; _item.name '_pdbx_nmr_ensemble.conformers_calculated_total_number' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code int loop_ _item_examples.case '40' _item_aliases.alias_name '_rcsb_nmr_ensemble.conformers_calculated_total_number' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.conformers_submitted_total_number _item_description.description ; The number of conformer (models) that are submitted for the ensemble. ; _item.name '_pdbx_nmr_ensemble.conformers_submitted_total_number' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code int loop_ _item_examples.case '20' _item_aliases.alias_name '_rcsb_nmr_ensemble.conformers_submitted_total_number' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.conformer_selection_criteria _item_description.description ; By highlighting the appropriate choice(s), describe how the submitted conformer (models) were selected. ; _item.name '_pdbx_nmr_ensemble.conformer_selection_criteria' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'structures with the lowest energy' 'structures with the least restraint violations' 'structures with acceptable covalent geometry' 'structures with favorable non-bond energy' 'target function' 'back calculated data agree with experimental NOESY spectrum' 'all calculated structures submitted' ; The submitted conformer models are the 25 structures with the lowest energy. ; ; The submitted conformer models are those with the fewest number of constraint violations. ; _item_aliases.alias_name '_rcsb_nmr_ensemble.conformer_selection_criteria' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.representative_conformer _item_description.description ; The number of the conformer identified as most representative. ; _item.name '_pdbx_nmr_ensemble.representative_conformer' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code int loop_ _item_examples.case '20' _item_aliases.alias_name '_rcsb_nmr_ensemble.representative_conformer' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.average_constraints_per_residue _item_description.description ; The average number of constraints per residue for the ensemble ; _item.name '_pdbx_nmr_ensemble.average_constraints_per_residue' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code int loop_ _item_examples.case '30.2' _item_aliases.alias_name '_rcsb_nmr_ensemble.average_constraints_per_residue' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.average_constraint_violations_per_residue _item_description.description ; The average number of constraint violations on a per residue basis for the ensemble. ; _item.name '_pdbx_nmr_ensemble.average_constraint_violations_per_residue' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code int loop_ _item_examples.case '0.25' _item_aliases.alias_name '_rcsb_nmr_ensemble.average_constraint_violations_per_residue' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.maximum_distance_constraint_violation _item_description.description ; The maximum distance constraint violation for the ensemble. ; _item.name '_pdbx_nmr_ensemble.maximum_distance_constraint_violation' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.4' _item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_distance_constraint_violation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.average_distance_constraint_violation _item_description.description ; The average distance restraint violation for the ensemble. ; _item.name '_pdbx_nmr_ensemble.average_distance_constraint_violation' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.11' _item_aliases.alias_name '_rcsb_nmr_ensemble.average_distance_constraint_violation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation _item_description.description ; The maximum upper distance constraint violation for the ensemble. ; _item.name '_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.4' _item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_upper_distance_constraint_violation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation _item_description.description ; The maximum lower distance constraint violation for the ensemble. ; _item.name '_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.3' _item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_lower_distance_constraint_violation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.distance_constraint_violation_method _item_description.description ; Describe the method used to calculate the distance constraint violation statistics, i.e. are they calculated over all the distance constraints or calculated for violations only? ; _item.name '_pdbx_nmr_ensemble.distance_constraint_violation_method' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Statistics were calculated over all of the distance constraints.' 'Statistics were calculated for violations only' _item_aliases.alias_name '_rcsb_nmr_ensemble.distance_constraint_violation_method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation _item_description.description ; The maximum torsion angle constraint violation for the ensemble. ; _item.name '_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '4' _item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_torsion_angle_constraint_violation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.average_torsion_angle_constraint_violation _item_description.description ; The average torsion angle constraint violation for the ensemble. ; _item.name '_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '2.4' _item_aliases.alias_name '_rcsb_nmr_ensemble.average_torsion_angle_constraint_violation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble.torsion_angle_constraint_violation_method _item_description.description ; This item describes the method used to calculate the torsion angle constraint violation statistics. i.e. are the entered values based on all torsion angle or calculated for violations only? ; _item.name '_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method' _item.category_id pdbx_nmr_ensemble _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Statistics were calculated over all the torsion angle constraints.' 'Statistics were calculated for torsion angle constraints violations only.' _item_aliases.alias_name '_rcsb_nmr_ensemble.torsion_angle_constraint_violation_method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ########################################################################## ### save_pdbx_nmr_ensemble_rms _category.description ; Structural statistics are derived from molecular dynamics and simulated annealing programs. ; _category.id pdbx_nmr_ensemble_rms _category.mandatory_code no _category_key.name '_pdbx_nmr_ensemble_rms.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example is derived from the MCP-1 structure calculation statistics. For this structure the statistics were calculated over residues 5-69 for both the monomer and dimer . ; # ; loop_ _pdbx_nmr_ensemble_rms.entry_id _pdbx_nmr_ensemble_rms.residue_range_begin _pdbx_nmr_ensemble_rms.chain_range_begin _pdbx_nmr_ensemble_rms.residue_range_end _pdbx_nmr_ensemble_rms.chain_range_end _pdbx_nmr_ensemble_rms.atom_type _pdbx_nmr_ensemble_rms.distance_rms_dev _pdbx_nmr_ensemble_rms.distance_rms_dev_error 1ABC 5 A 69 A 'all heavy atoms' 0.22 0.06 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_ensemble_rms.entry_id _item_description.description ; '?' ; _item.name '_pdbx_nmr_ensemble_rms.entry_id' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nmr_ensemble_rms.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.residue_range_begin _item_description.description ; Structure statistics are often calculated only over the well-ordered region(s) of the biopolymer. Portions of the macromolecule are often mobile and disordered, hence they are excluded in calculating the statistics. To define the range(s) over which the statistics are calculated, enter the beginning residue number(s): e.g. if the regions used were 5-32 and 41-69, enter 5,41 ; _item.name '_pdbx_nmr_ensemble_rms.residue_range_begin' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code int loop_ _item_examples.case 5 41 _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.residue_range_begin' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.chain_range_begin _item_description.description ; The beginning chain id. ; _item.name '_pdbx_nmr_ensemble_rms.chain_range_begin' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code code _item_examples.case A _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.chain_range_begin' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.residue_range_end _item_description.description ; The ending residue number: e.g. 32,69. ; _item.name '_pdbx_nmr_ensemble_rms.residue_range_end' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code int loop_ _item_examples.case 32 69 _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.residue_range_end' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.chain_range_end _item_description.description ; The ending chain id: ; _item.name '_pdbx_nmr_ensemble_rms.chain_range_end' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code code _item_examples.case A _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.chain_range_end' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.atom_type _item_description.description ; Statistics are often calculated over only some of the atoms, e.g. backbone, or heavy atoms. Describe which type of atoms are used for the statistical analysis. ; _item.name '_pdbx_nmr_ensemble_rms.atom_type' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'backbone atoms' 'heavy atoms' loop_ _item_enumeration.value 'backbone heavy atoms' 'side chain heavy atoms' 'all heavy atoms' 'all atoms' 'all backbone atoms' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.atom_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.distance_rms_dev _item_description.description ; The distance rmsd to the mean structure for the ensemble of structures. ; _item.name '_pdbx_nmr_ensemble_rms.distance_rms_dev' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.22' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.distance_rms_dev' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.distance_rms_dev_error _item_description.description ; The error in the distance rmsd. ; _item.name '_pdbx_nmr_ensemble_rms.distance_rms_dev_error' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.07' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.distance_rms_dev_error' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.covalent_bond_rms_dev _item_description.description ; The covalent bond rmsd to the target value for the ensemble. ; _item.name '_pdbx_nmr_ensemble_rms.covalent_bond_rms_dev' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.0066' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.covalent_bond_rms_dev' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error _item_description.description ; The error in the covalent bond rmsd. ; _item.name '_pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.0001' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.covalent_bond_rms_dev_error' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.bond_angle_rms_dev _item_description.description ; The bond angle rmsd to the target values for the ensemble. ; _item.name '_pdbx_nmr_ensemble_rms.bond_angle_rms_dev' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '0.60' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.bond_angle_rms_dev' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error _item_description.description ; The error in the bond angle rmsd. ; _item.name '_pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '0.01' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.bond_angle_rms_dev_error' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev _item_description.description ; The improper torsion angle rmsd to the target values for the ensemble. ; _item.name '_pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '0.64' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.improper_torsion_angle_rms_dev' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error _item_description.description ; The error in the improper torsion angle rmsd. ; _item.name '_pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '0.04' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev _item_description.description ; The peptide planarity rmsd. ; _item.name '_pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.11' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.peptide_planarity_rms_dev' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error _item_description.description ; The error in the peptide planarity rmsd. ; _item.name '_pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_examples.case '0.05' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.peptide_planarity_rms_dev_error' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev _item_description.description ; The dihedral angle rmsd to the target values for the ensemble. ; _item.name '_pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '0.66' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.dihedral_angles_rms_dev' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error _item_description.description ; The error of the rmsd dihedral angles. ; _item.name '_pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code float _item_units.code degrees loop_ _item_examples.case '0.07' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.dihedral_angles_rms_dev_error' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_ensemble_rms.coord_average_rmsd_method _item_description.description ; Describe the method for calculating the coordinate average rmsd. ; _item.name '_pdbx_nmr_ensemble_rms.coord_average_rmsd_method' _item.category_id pdbx_nmr_ensemble_rms _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Replace with item example text' _item_aliases.alias_name '_rcsb_nmr_ensemble_rms.coord_average_rmsd_method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### ########################################################################## ### save_pdbx_nmr_representative _category.description ; An average structure is often calculated in addition to the ensemble, or one of the ensemble is selected as a representative structure. This section describes selection of the representative structure. ; _category.id pdbx_nmr_representative _category.mandatory_code no _category_key.name '_pdbx_nmr_representative.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example is drawn from the MCP-1 structure. ; # ; _pdbx_nmr_representative.entry_id 1ABC _pdbx_nmr_representative.conformer_id 15 _pdbx_nmr_representative.selection_criteria 'lowest energy' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_nmr_representative.entry_id _item_description.description ; msd will assign the ID. ; _item.name '_pdbx_nmr_representative.entry_id' _item.category_id pdbx_nmr_representative _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nmr_representative.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_rcsb_nmr_representative.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_representative.conformer_id _item_description.description ; If a member of the ensemble has been selected as a representative structure, identify it by its model number. ; _item.name '_pdbx_nmr_representative.conformer_id' _item.category_id pdbx_nmr_representative _item.mandatory_code no _item_type.code line loop_ _item_examples.case '15' _item_aliases.alias_name '_rcsb_nmr_representative.conformer_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_representative.selection_criteria _item_description.description ; By highlighting the appropriate choice(s), describe the criteria used to select this structure as a representative structure, or if an average structure has been calculated describe how this was done. ; _item.name '_pdbx_nmr_representative.selection_criteria' _item.category_id pdbx_nmr_representative _item.mandatory_code no _item_type.code line # loop_ # _item_enumeration.value # 'closest to the average' # 'lowest energy' # 'fewest violations' # 'minimized average structure' _item_examples.case ; The structure closest to the average. The structure with the lowest energy was selected. The structure with the fewest number of violations was selected. A minimized average structure was calculated. ; _item_aliases.alias_name '_rcsb_nmr_representative.selection_criteria' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save_pdbx_nmr_refine _category.description ; Describe the method and details of the refinement of the deposited structure. ; _category.id pdbx_nmr_refine _category.mandatory_code no _category_key.name '_pdbx_nmr_refine.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; This example is drawn from the MCP-1 structure. ; ; loop_ _pdbx_nmr_refine.entry_id _pdbx_nmr_refine.method 1ABC 'torsion angle dynamics' ; save_ save__pdbx_nmr_refine.entry_id _item_description.description ; You can leave this blank as an ID will be assigned by the RCSB to the constraint file. ; _item.name '_pdbx_nmr_refine.entry_id' _item.category_id pdbx_nmr_refine _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nmr_refine.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_rcsb_nmr_refine.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_refine.method _item_description.description ; The method used to determine the structure. ; _item.name '_pdbx_nmr_refine.method' _item.category_id pdbx_nmr_refine _item.mandatory_code yes _item_type.code text _item_examples.case ; distance geometry simulated annealing molecular dynamics matrix relaxation torsion angle dynamics ; _item_aliases.alias_name '_rcsb_nmr_refine.method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_refine.details _item_description.description ; Additional details about the NMR refinement. ; _item.name '_pdbx_nmr_refine.details' _item.category_id pdbx_nmr_refine _item.mandatory_code no _item_type.code text _item_examples.case ; Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 3344 restraints, 3167 are NOE-derived distance constraints, 68 dihedral angle restraints,109 distance restraints from hydrogen bonds. ; _item_aliases.alias_name '_rcsb_nmr_refine.details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ## save_pdbx_nmr_force_constants _category.description ; The final force constants, including units, employed for the various experimental constraints, covalent geometry constraints, and the non-bonded interaction terms in the target function used for simulated annealing. ; _category.id pdbx_nmr_force_constants _category.mandatory_code no loop_ _category_key.name '_pdbx_nmr_force_constants.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - ; This example is taken from a study of BAF, a dimeric DNA binding protein. The final force constants in the target function used for simulated annealing are: Experimental Constraint terms: Distance (NOE,H-bonds), Torsion angles, J coupling, 13C shifts, 1H shifts, Dipolar coupling, D isotope shifts Covalent Geometry Constraint terms: Bond lengths, Angles, Impropers Non-bonded Interaction terms: van der Waals, Type of van der Waals term, Conformational database potential, Radius of gyration. ; # ; _pdbx_nmr_force_constants.entry_id 1ABC _pdbx_nmr_force_constants.exptl_distance_term 30. _pdbx_nmr_force_constants.exptl_distance_term_units 'kcal/mol/A**2' _pdbx_nmr_force_constants.exptl_torsion_angles_term 200. _pdbx_nmr_force_constants.exptl_torsion_angles_term_units 'kcal/mol/rad**2' _pdbx_nmr_force_constants.exptl_J_coupling_term 1. _pdbx_nmr_force_constants.exptl_J_coupling_term_units 'kcal/mol/Hz**2' _pdbx_nmr_force_constants.exptl_13C_shift_term 0.5 _pdbx_nmr_force_constants.exptl_13C_shift_term_units 'kcal/mol/ppm**2' _pdbx_nmr_force_constants.exptl_1H_shift_term 7.5 _pdbx_nmr_force_constants.exptl_1H_shift_term_units 'kcal/mol/ppm**2' _pdbx_nmr_force_constants.covalent_geom_bond_term 1000. _pdbx_nmr_force_constants.covalent_geom_bond_term_units 'kcal/mol/A**2' _pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type 4. _pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type_units 'kcal/mol/A**4' ; save_ save__pdbx_nmr_force_constants.entry_id _item_description.description ; You can leave this blank as an ID will be assigned by the RCSB. ; _item.name '_pdbx_nmr_force_constants.entry_id' _item.category_id pdbx_nmr_force_constants _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_nmr_force_constants.entry_id' _item_linked.parent_name '_entry.id' _item_aliases.alias_name '_rcsb_nmr_force_constants.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_distance_term _item_description.description ; The final force constant for distance (NOEs) constraints term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.exptl_distance_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '30' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_distance_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__pdbx_nmr_force_constants.exptl_distance_term_units _item_description.description ; The units for the force constant for the distance constraints term. ; _item.name '_pdbx_nmr_force_constants.exptl_distance_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/ A**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/A**2' 'kilocalories per mole per square angstrom' 'kJ/mol/nm**2' 'kilojoules per mole per square nanometer' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_distance_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_torsion_angles_term _item_description.description ; The final force constant for the torsion angle term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.exptl_torsion_angles_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '200' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_torsion_angles_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_torsion_angles_term_units _item_description.description ; The units for the force constant for the torsion angle constraints term. ; _item.name '_pdbx_nmr_force_constants.exptl_torsion_angles_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/rad**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/rad**2' 'kilocalories per mole per square radian' 'kJ/mol/rad**2' 'kilojoules per mole per square radian' 'author' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_torsion_angles_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__pdbx_nmr_force_constants.exptl_J_coupling_term _item_description.description ; The final force constant for J coupling term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.exptl_J_coupling_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '1' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_J_coupling_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_J_coupling_term_units _item_description.description ; The units for the force constant for the J coupling term. ; _item.name '_pdbx_nmr_force_constants.exptl_J_coupling_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/Hz**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/Hz**2' 'kilocalories per mole per square angstrom' 'kJ/mol/Hz**2' 'kilojoules per mole per square nanometer' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_J_coupling_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_13C_shift_term _item_description.description ; The final force constant for 13C shift constraints term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.exptl_13C_shift_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '0.5' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_13C_shift_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_13C_shift_term_units _item_description.description ; The units for the force constant for the 13C shift constraints term. ; _item.name '_pdbx_nmr_force_constants.exptl_13C_shift_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/ppm**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/ppm**2' 'kilocalories per mole per part per million squared' 'kJ/mol/ppm**2' 'kilojoules per mole per part per million squared' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_13C_shift_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save__pdbx_nmr_force_constants.exptl_1H_shift_term _item_description.description ; The final force constant for 1H shift constraints term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.exptl_1H_shift_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '7.5' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_1H_shift_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_1H_shift_term_units _item_description.description ; The units for the force constant for the 1H shift constraints term. ; _item.name '_pdbx_nmr_force_constants.exptl_1H_shift_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/ppm**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/ppm**2' 'kilocalories per mole per part per million squared' 'kJ/mol/ppm**2' 'kilojoules per mole per part per million squared' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_1H_shift_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_dipolar_coupling_term _item_description.description ; The final force constant for dipolar coupling constraint term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.exptl_dipolar_coupling_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '1' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_dipolar_coupling_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_dipolar_coupling_term_units _item_description.description ; The units for the force constant for the dipolar coupling constraints term. ; _item.name '_pdbx_nmr_force_constants.exptl_dipolar_coupling_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/Hz**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/Hz**2' 'kilocalories per mole per Hertz squared' 'kJ/mol/Hz**2' 'kilojoules per mole per Hertz squared' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_dipolar_coupling_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.exptl_D_isotope_shift_term _item_description.description ; The final force constant for Deuterium isotope shift constraints term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.exptl_D_isotope_shift_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '0.5' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_D_isotope_shift_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### ### NEXT save__pdbx_nmr_force_constants.exptl_D_isotope_shift_term_units _item_description.description ; The units for the force constant for the Deuterium isotope shift constraints term. ; _item.name '_pdbx_nmr_force_constants.exptl_D_isotope_shift_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/ppb**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/ppb**2' 'kilocalories per mole per part per billion squared' 'kJ/mol/ppb**2' 'kilojoules per mole per part per billion squared' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_D_isotope_shift_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.covalent_geom_bond_term _item_description.description ; The final force constant for the covalent geometry bond length constraints term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.covalent_geom_bond_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '1000' _item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_bond_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.covalent_geom_bond_term_units _item_description.description ; The units for the force constant for the covalent geometry bond length constraints term. ; _item.name '_pdbx_nmr_force_constants.covalent_geom_bond_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/A**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/A**2' 'kilocalories per mole per square angstrom' 'kJ/mol/nm**2' 'kilojoules per mole per square nanometer' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_bond_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.covalent_geom_angles_term _item_description.description ; The final force constant for covalent geometry angle constraints term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.covalent_geom_angles_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '500' _item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_angles_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.covalent_geom_angles_term_units _item_description.description ; The units for the force constant for the covalent geometry angle constraints term. ; _item.name '_pdbx_nmr_force_constants.covalent_geom_angles_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/rad**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/rad**2' 'kilocalories per mole per radian squared' 'kJ/mol/rad**2' 'kilojoules per mole per radian squared' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_angles_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.covalent_geom_impropers_term _item_description.description ; The final force constant for covalent geometry impropers contstraints term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.covalent_geom_impropers_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '500' _item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_impropers_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.covalent_geom_impropers_term_units _item_description.description ; The units for the force constant for the covalent geometry impropers constraints term. ; _item.name '_pdbx_nmr_force_constants.covalent_geom_impropers_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/rad**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/rad**2' 'kilocalories per mole per radian squared' 'kJ/mol/rad**2' 'kilojoules per mole per radian squared' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_impropers_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type _item_description.description ; The type of van der Waals term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'quartic' loop_ _item_enumeration.value 'quartic' 'other' _item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term _item_description.description ; The force constant used for the non-bonded interaction van der Waals term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '4' _item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_van_der_Waals_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_units _item_description.description ; The units for the force constant for the van der Waals term. ; _item.name '_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/ A**4' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/A**4' 'kilocalories per mole per Angstrom to the 4th power' 'kJ/mol/nm**4' 'kilojoules per mole per nanometer to the 4th power' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_van_der_Waals_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.non-bonded_inter_conf_db_potential_term _item_description.description ; The force constant used for the non-bonded interaction conformational database potential term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.non-bonded_inter_conf_db_potential_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '1.0' _item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_conf_db_potential_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term _item_description.description ; The force constant used for the non-bonded interaction radius of gyration term employed in the target function used for simulated annealing. ; _item.name '_pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code float loop_ _item_examples.case '100' _item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_radius_of_gyration_term' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term_units _item_description.description ; The units for the force constant for the radius of gyration term. ; _item.name '_pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term_units' _item.category_id pdbx_nmr_force_constants _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'kcal/mol/ A**2' loop_ _item_enumeration.value _item_enumeration.detail 'kcal/mol/ A**2' 'kilocalories per mole per square Angstrom' 'kJ/mol/ nm**4' 'kilojoules per mole per square nanometer' 'other' 'author added units' _item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_radius_of_gyration_term_units' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ### EOF mmcif_pdbx-def-2.dic########################################################################### # # File: mmcif_pdbx-def-4.dic # # PDB Exchange Data Dictionary # # This data dictionary contains definitions used by wwPDB for data exchange # and data processing. # # Definition Section 4 # # ########################################################################### ## ## Additional aliases required only for NDB/RCSB use: ## save__refine.overall_SU_B # _item.name '_refine.overall_SU_B' # _item.category_id refine # _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_ESU_B' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 # _item_type.code float save_ save__refine.overall_SU_ML # _item.name '_refine.overall_SU_ML' # _item.category_id refine # _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_ESU_ML' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 # _item_type.code float save_ save__refine_hist.number_atoms_solvent # _item.name '_refine_hist.number_atoms_solvent' # _item.category_id refine_hist # _item.mandatory_code no _item_aliases.alias_name '_refine_hist.rcsb_number_atoms_solvent' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 # _item_type.code int save_ save__refine_hist.number_atoms_total # _item.name '_refine_hist.number_atoms_total' # _item.category_id refine_hist # _item.mandatory_code no _item_aliases.alias_name '_refine_hist.rcsb_number_atoms_total' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 # _item_type.code int save_ ## ## NDB Specific definitions ## ########################## ## NDB_STRUCT_CONF_NA ## ########################## save_ndb_struct_conf_na _category.description ; Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry. ; _category.id ndb_struct_conf_na _category.mandatory_code no loop_ _category_key.name '_ndb_struct_conf_na.entry_id' '_ndb_struct_conf_na.feature' loop_ _category_group.id 'inclusive_group' 'struct_group' 'ndb_group' _ndb_category_examples.case ; loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature _ndb_struct_conf_na.feature_count rcsb000001 'double helix' 1 rcsb000001 'b-form double helix' 1 rcsb000001 'quadruple helix' 1 ; save_ save__ndb_struct_conf_na.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_ndb_struct_conf_na.entry_id' _item.category_id ndb_struct_conf_na _item.mandatory_code yes _item_linked.child_name '_ndb_struct_conf_na.entry_id' _item_linked.parent_name '_entry.id' save_ save__ndb_struct_conf_na.feature _item_description.description ; This data item identifies a secondary structure feature of this entry. ; _item.name '_ndb_struct_conf_na.feature' _item.category_id ndb_struct_conf_na _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'double helix' . 'a-form double helix' . 'b-form double helix' . 'z-form double helix' . 'other right-handed double helix' . 'triple helix' . 'quadruple helix' . 'parallel strands' . 'internal loop' . 'bulge loop' . 'tetraloop' . 'hairpin loop' . 'two-way junction' . 'three-way junction' . 'four-way junction' . 'mismatched base pair' . save_ save__ndb_struct_conf_na.feature_count _item_description.description ; This data item counts the number of occurences of this feature in this entry. ; _item.name '_ndb_struct_conf_na.feature_count' _item.category_id ndb_struct_conf_na _item.mandatory_code no _item_type.code int save_ ############################# ## NDB_STRUCT_FEATURE_NA ## ############################# save_ndb_struct_feature_na _category.description ; Data items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry. ; _category.id ndb_struct_feature_na _category.mandatory_code no loop_ _category_key.name '_ndb_struct_feature_na.entry_id' '_ndb_struct_feature_na.feature' loop_ _category_group.id 'inclusive_group' 'struct_group' 'ndb_group' _ndb_category_examples.case ; loop_ _ndb_struct_feature_na.entry_id _ndb_struct_feature_na.feature _ndb_struct_feature_na.feature_count rcsb000001 'intercalated base' 1 rcsb000001 'bent/kinked double helix' 1 ; save_ save__ndb_struct_feature_na.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_ndb_struct_feature_na.entry_id' _item.category_id ndb_struct_feature_na _item.mandatory_code yes _item_linked.child_name '_ndb_struct_feature_na.entry_id' _item_linked.parent_name '_entry.id' save_ save__ndb_struct_feature_na.feature _item_description.description ; This data item identifies a structural feature of this entry. ; _item.name '_ndb_struct_feature_na.feature' _item.category_id ndb_struct_feature_na _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'pseudoknot' . 'intercalated base' . 'backbone turn' . 'intramolecular base triplet' . 'ribose zipper' . 'purine platform' . 'bent/kinked double helix' . save_ save__ndb_struct_feature_na.feature_count _item_description.description ; This data item counts the number of occurences of this feature in this entry. ; _item.name '_ndb_struct_feature_na.feature_count' _item.category_id ndb_struct_feature_na _item.mandatory_code no _item_type.code int save_ ############################# ## NDB_STRUCT_NA_BASE_PAIR ## ############################# save_ndb_struct_na_base_pair _category.description ; Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions. ; _category.id ndb_struct_na_base_pair _category.mandatory_code no loop_ _category_key.name '_ndb_struct_na_base_pair.model_number' '_ndb_struct_na_base_pair.i_label_comp_id' '_ndb_struct_na_base_pair.i_label_asym_id' '_ndb_struct_na_base_pair.i_label_seq_id' '_ndb_struct_na_base_pair.i_symmetry' '_ndb_struct_na_base_pair.j_label_comp_id' '_ndb_struct_na_base_pair.j_label_asym_id' '_ndb_struct_na_base_pair.j_label_seq_id' '_ndb_struct_na_base_pair.j_symmetry' loop_ _category_group.id 'inclusive_group' 'struct_group' 'ndb_group' loop_ _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening 1 G A 1 1_555 C A 8 7_555 -0.396 -0.156 -0.018 -5.523 -6.752 -3.291 1 G A 2 1_555 C A 7 7_555 -0.094 -0.220 -0.334 -4.727 -9.765 2.311 1 G A 3 1_555 C A 6 7_555 -0.285 -0.239 0.008 -6.454 -12.575 -1.181 # ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_struct_na_base_pair.model_number _item_description.description ; Describes the model number of the the base pair. This data item is a pointer to _atom_site.ndb_model in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.model_number' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.model_number' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' save_ save__ndb_struct_na_base_pair.pair_number _item_description.description ; Sequential number of pair in the pair sequence. ; _item.name '_ndb_struct_na_base_pair.pair_number' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code int save_ save__ndb_struct_na_base_pair.pair_name _item_description.description ; Text label for this base pair. ; _item.name '_ndb_struct_na_base_pair.pair_name' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code line save_ save__ndb_struct_na_base_pair.i_label_asym_id _item_description.description ; Describes the asym id of the i-th base in the base pair. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.i_label_asym_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.i_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_na_base_pair.i_label_comp_id _item_description.description ; Describes the component id of the i-th base in the base pair. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.i_label_comp_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.i_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_na_base_pair.i_label_seq_id _item_description.description ; Describes the sequence number of the i-th base in the base pair. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.i_label_seq_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.i_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_na_base_pair.i_symmetry _item_description.description ; Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the base pair. ; _item.name '_ndb_struct_na_base_pair.i_symmetry' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__ndb_struct_na_base_pair.j_label_asym_id _item_description.description ; Describes the asym id of the j-th base in the base pair. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.j_label_asym_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.j_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_na_base_pair.j_label_comp_id _item_description.description ; Describes the component id of the j-th base in the base pair. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.j_label_comp_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.j_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_na_base_pair.j_label_seq_id _item_description.description ; Describes the sequence number of the j-th base in the base pair. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.j_label_seq_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.j_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_na_base_pair.j_symmetry _item_description.description ; Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the base pair. ; _item.name '_ndb_struct_na_base_pair.j_symmetry' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__ndb_struct_na_base_pair.i_auth_asym_id _item_description.description ; Describes the asym id of the i-th base in the base pair. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.i_auth_asym_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.i_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_na_base_pair.i_auth_seq_id _item_description.description ; Describes the sequence number of the i-th base in the base pair. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.i_auth_seq_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.i_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_na_base_pair.i_PDB_ins_code _item_description.description ; Describes the PDB insertion code of the i-th base in the base pair. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.i_PDB_ins_code' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code # _item_linked.child_name '_ndb_struct_na_base_pair.i_PDB_ins_code' # _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ save__ndb_struct_na_base_pair.j_auth_asym_id _item_description.description ; Describes the asym id of the j-th base in the base pair. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.j_auth_asym_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.j_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_na_base_pair.j_auth_seq_id _item_description.description ; Describes the sequence number of the j-th base in the base pair. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.j_auth_seq_id' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair.j_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_na_base_pair.j_PDB_ins_code _item_description.description ; Describes the PDB insertion code of the j-th base in the base pair. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair.j_PDB_ins_code' _item.category_id ndb_struct_na_base_pair _item.mandatory_code yes _item_type.code code # _item_linked.child_name '_ndb_struct_na_base_pair.j_PDB_ins_code' # _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ save__ndb_struct_na_base_pair.shear _item_description.description ; The value of the base pair shear parameter. ; _item.name '_ndb_struct_na_base_pair.shear' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair.stretch _item_description.description ; The value of the base pair stretch parameter. ; _item.name '_ndb_struct_na_base_pair.stretch' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair.stagger _item_description.description ; The value of the base pair stagger parameter. ; _item.name '_ndb_struct_na_base_pair.stagger' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair.buckle _item_description.description ; The value of the base pair buckle parameter. ; _item.name '_ndb_struct_na_base_pair.buckle' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair.propeller _item_description.description ; The value of the base pair propeller parameter. ; _item.name '_ndb_struct_na_base_pair.propeller' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair.opening _item_description.description ; The value of the base pair opening parameter. ; _item.name '_ndb_struct_na_base_pair.opening' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair.hbond_type_12 _item_description.description ; Base pair classification of Westhoff and Leontis. ; _item.name '_ndb_struct_na_base_pair.hbond_type_12' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code int save_ save__ndb_struct_na_base_pair.hbond_type_28 _item_description.description ; Base pair classification of Saenger ; _item.name '_ndb_struct_na_base_pair.hbond_type_28' _item.category_id ndb_struct_na_base_pair _item.mandatory_code no _item_type.code int save_ ################################## ## NDB_STRUCT_NA_BASE_PAIR_STEP ## ################################## save_ndb_struct_na_base_pair_step _category.description ; Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions. ; _category.id ndb_struct_na_base_pair_step _category.mandatory_code no loop_ _category_key.name '_ndb_struct_na_base_pair_step.model_number' '_ndb_struct_na_base_pair_step.i_label_comp_id_1' '_ndb_struct_na_base_pair_step.i_label_asym_id_1' '_ndb_struct_na_base_pair_step.i_label_seq_id_1' '_ndb_struct_na_base_pair_step.i_symmetry_1' '_ndb_struct_na_base_pair_step.j_label_comp_id_1' '_ndb_struct_na_base_pair_step.j_label_asym_id_1' '_ndb_struct_na_base_pair_step.j_label_seq_id_1' '_ndb_struct_na_base_pair_step.j_symmetry_1' '_ndb_struct_na_base_pair_step.i_label_comp_id_2' '_ndb_struct_na_base_pair_step.i_label_asym_id_2' '_ndb_struct_na_base_pair_step.i_label_seq_id_2' '_ndb_struct_na_base_pair_step.i_symmetry_2' '_ndb_struct_na_base_pair_step.j_label_comp_id_2' '_ndb_struct_na_base_pair_step.j_label_asym_id_2' '_ndb_struct_na_base_pair_step.j_label_seq_id_2' '_ndb_struct_na_base_pair_step.j_symmetry_2' loop_ _category_group.id 'inclusive_group' 'struct_group' 'ndb_group' loop_ _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist 1 G A 1 1_555 C A 8 7_555 G A 2 1_555 C A 7 7_555 0.369 -1.414 3.339 3.056 9.755 33.530 1 G A 2 1_555 C A 7 7_555 G A 3 1_555 C A 6 7_555 0.176 -1.672 3.371 -1.176 6.725 30.004 # ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_struct_na_base_pair_step.model_number _item_description.description ; Describes the model number of the the base pair step. This data item is a pointer to _atom_site.ndb_model in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.model_number' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.model_number' _item_linked.parent_name '_atom_site.pdbx_PDB_model_num' save_ save__ndb_struct_na_base_pair_step.step_number _item_description.description ; The sequence number of this step in the step sequence. ; _item.name '_ndb_struct_na_base_pair_step.step_number' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code int save_ save__ndb_struct_na_base_pair_step.step_name _item_description.description ; The text name of this step. ; _item.name '_ndb_struct_na_base_pair_step.step_name' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code line save_ save__ndb_struct_na_base_pair_step.i_label_asym_id_1 _item_description.description ; Describes the asym id of the i-th base in the first base pair of the step. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_label_asym_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_asym_id_1' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_na_base_pair_step.i_label_comp_id_1 _item_description.description ; Describes the component id of the i-th base in the first base pair of the step. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_label_comp_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_comp_id_1' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_na_base_pair_step.i_label_seq_id_1 _item_description.description ; Describes the sequence number of the i-th base in the first base pair of the step. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_label_seq_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_seq_id_1' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_na_base_pair_step.i_symmetry_1 _item_description.description ; Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the first base pair of the step. ; _item.name '_ndb_struct_na_base_pair_step.i_symmetry_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__ndb_struct_na_base_pair_step.j_label_asym_id_1 _item_description.description ; Describes the asym id of the j-th base in the first base pair of the step. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_label_asym_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_asym_id_1' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_na_base_pair_step.j_label_comp_id_1 _item_description.description ; Describes the component id of the j-th base in the first base pair of the step. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_label_comp_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_comp_id_1' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_na_base_pair_step.j_label_seq_id_1 _item_description.description ; Describes the sequence number of the j-th base in the first base pair of the step. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_label_seq_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_seq_id_1' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_na_base_pair_step.j_symmetry_1 _item_description.description ; Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the first base pair of the step. ; _item.name '_ndb_struct_na_base_pair_step.j_symmetry_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__ndb_struct_na_base_pair_step.i_label_asym_id_2 _item_description.description ; Describes the asym id of the i-th base in the second base pair of the step. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_label_asym_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_asym_id_2' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_na_base_pair_step.i_label_comp_id_2 _item_description.description ; Describes the component id of the i-th base in the second base pair of the step. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_label_comp_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_comp_id_2' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_na_base_pair_step.i_label_seq_id_2 _item_description.description ; Describes the sequence number of the i-th base in the second base pair of the step. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_label_seq_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_seq_id_2' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_na_base_pair_step.i_symmetry_2 _item_description.description ; Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the second base pair of the step. ; _item.name '_ndb_struct_na_base_pair_step.i_symmetry_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__ndb_struct_na_base_pair_step.j_label_asym_id_2 _item_description.description ; Describes the asym id of the j-th base in the second base pair of the step. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_label_asym_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_asym_id_2' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ndb_struct_na_base_pair_step.j_label_comp_id_2 _item_description.description ; Describes the component id of the j-th base in the second base pair of the step. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_label_comp_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_comp_id_2' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ndb_struct_na_base_pair_step.j_label_seq_id_2 _item_description.description ; Describes the sequence number of the j-th base in the second base pair of the step. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_label_seq_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_seq_id_2' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ndb_struct_na_base_pair_step.j_symmetry_2 _item_description.description ; Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the second base pair of the step. ; _item.name '_ndb_struct_na_base_pair_step.j_symmetry_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__ndb_struct_na_base_pair_step.i_auth_asym_id_1 _item_description.description ; Describes the author's asym id of the i-th base in the first base pair of the step. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_auth_asym_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_asym_id_1' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_na_base_pair_step.i_auth_seq_id_1 _item_description.description ; Describes the author's sequence number of the i-th base in the first base pair of the step. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_auth_seq_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_seq_id_1' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _item_description.description ; Describes the PDB insertion code of the i-th base in the first base pair of the step. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code # _item_linked.child_name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_1' # _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ save__ndb_struct_na_base_pair_step.j_auth_asym_id_1 _item_description.description ; Describes the author's asym id of the j-th base in the first base pair of the step. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_auth_asym_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_asym_id_1' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_na_base_pair_step.j_auth_seq_id_1 _item_description.description ; Describes the author's sequence number of the j-th base in the first base pair of the step. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_auth_seq_id_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_seq_id_1' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _item_description.description ; Describes the PDB insertion code of the j-th base in the first base pair of the step. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_1' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code # _item_linked.child_name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_1' # _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ save__ndb_struct_na_base_pair_step.i_auth_asym_id_2 _item_description.description ; Describes the author's asym id of the i-th base in the second base pair of the step. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_auth_asym_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_asym_id_2' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_na_base_pair_step.i_auth_seq_id_2 _item_description.description ; Describes the author's sequence number of the i-th base in the second base pair of the step. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_auth_seq_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_seq_id_2' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _item_description.description ; Describes the PDB insertion code of the i-th base in the second base pair of the step. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code # _item_linked.child_name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_2' # _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ save__ndb_struct_na_base_pair_step.j_auth_asym_id_2 _item_description.description ; Describes the author's asym id of the j-th base in the second base pair of the step. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_auth_asym_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_asym_id_2' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__ndb_struct_na_base_pair_step.j_auth_seq_id_2 _item_description.description ; Describes the author's sequence number of the j-th base in the second base pair of the step. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_auth_seq_id_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_seq_id_2' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__ndb_struct_na_base_pair_step.j_PDB_ins_code_2 _item_description.description ; Describes the PDB insertion code of the j-th base in the second base pair of the step. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category. ; _item.name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_2' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code yes _item_type.code code # _item_linked.child_name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_2' # _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' save_ save__ndb_struct_na_base_pair_step.shift _item_description.description ; The value of the base pair step shift parameter. ; _item.name '_ndb_struct_na_base_pair_step.shift' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.slide _item_description.description ; The value of the base pair step slide parameter. ; _item.name '_ndb_struct_na_base_pair_step.slide' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.rise _item_description.description ; The value of the base pair step rise parameter. ; _item.name '_ndb_struct_na_base_pair_step.rise' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.tilt _item_description.description ; The value of the base pair step tilt parameter. ; _item.name '_ndb_struct_na_base_pair_step.tilt' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.roll _item_description.description ; The value of the base pair step roll parameter. ; _item.name '_ndb_struct_na_base_pair_step.roll' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.twist _item_description.description ; The value of the base pair step twist parameter. ; _item.name '_ndb_struct_na_base_pair_step.twist' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.x_displacement _item_description.description ; The value of the base pair step X displacement parameter. ; _item.name '_ndb_struct_na_base_pair_step.x_displacement' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.y_displacement _item_description.description ; The value of the base pair step Y displacement parameter. ; _item.name '_ndb_struct_na_base_pair_step.y_displacement' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.helical_rise _item_description.description ; The value of the base pair step helical rise parameter. ; _item.name '_ndb_struct_na_base_pair_step.helical_rise' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.inclination _item_description.description ; The value of the base pair step inclination parameter. ; _item.name '_ndb_struct_na_base_pair_step.inclination' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.tip _item_description.description ; The value of the base pair step twist parameter. ; _item.name '_ndb_struct_na_base_pair_step.tip' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ save__ndb_struct_na_base_pair_step.helical_twist _item_description.description ; The value of the base pair step helical twist parameter. ; _item.name '_ndb_struct_na_base_pair_step.helical_twist' _item.category_id ndb_struct_na_base_pair_step _item.mandatory_code no _item_type.code float save_ ## ## save_ndb_original_ndb_coordinates _category.description ; Placeholder category for PDB coordinate data. ; _category.id ndb_original_ndb_coordinates _category.mandatory_code no loop_ _category_key.name '_ndb_original_ndb_coordinates.coord_section' loop_ _category_group.id 'inclusive_group' 'ndb_group' save_ save__ndb_original_ndb_coordinates.coord_section _item_description.description ; ; _item.name '_ndb_original_ndb_coordinates.coord_section' _item.category_id ndb_original_ndb_coordinates _item.mandatory_code yes _item_type.code text save_ ## ## save_pdbx_entity_nonpoly _category.description ; ; _category.id pdbx_entity_nonpoly _category.mandatory_code no _category_key.name '_pdbx_entity_nonpoly.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' 'rcsb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_entity_nonpoly.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_pdbx_entity_nonpoly.entity_id' _item.category_id pdbx_entity_nonpoly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_entity_nonpoly.entity_id' _item_linked.parent_name '_entity.id' _item_aliases.alias_name '_rcsb_entity_nonpoly.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_nonpoly.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_pdbx_entity_nonpoly.comp_id' _item.category_id pdbx_entity_nonpoly _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_entity_nonpoly.comp_id' _item_linked.parent_name '_chem_comp.id' _item_aliases.alias_name '_rcsb_entity_nonpoly.comp_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_entity_nonpoly.name _item_description.description ; A name for the non-polymer entity ; _item.name '_pdbx_entity_nonpoly.name' _item.category_id pdbx_entity_nonpoly _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_rcsb_entity_nonpoly.name' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ # ### EOF mmcif_pdbx-def-4.dic ########################################################################### # # File: mmcif_pdbx-def-5.dic # # PDB Exchange Data Dictionary # # This data dictionary contains definitions used by wwPDB for data exchange # and data processing. # # Definition Section 5 # This section primarily contains extensions for # data extraction by PDB_EXTRACT. # ########################################################################### save_pdbx_phasing_dm _category.description ; Data items in the PDBX_PHASING_DM category record details about density modification ; _category.id pdbx_phasing_dm _category.mandatory_code no _category_key.name '_pdbx_phasing_dm.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - density modification from resolve ; ; _pdbx_phasing_dm.entry_id ABC001 _pdbx_phasing_dm.fom_acentric 0.85 _pdbx_phasing_dm.fom_centric 0.79 _pdbx_phasing_dm.fom 0.85 _pdbx_phasing_dm.reflns_acentric 11351 _pdbx_phasing_dm.reflns_centric 1135 _pdbx_phasing_dm.reflns 12486 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_phasing_dm.entry_id _item_description.description ; The value of _pdbx_phasing_dm.entry_id identifies the data block. ; _item.name '_pdbx_phasing_dm.entry_id' _item.category_id pdbx_phasing_dm _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_pdbx_phasing_dm.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.method _item_description.description ; The value of _pdbx_phasing_dm.method identifies the method used for density modification ; _item.name '_pdbx_phasing_dm.method' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_pdbx_phasing_dm.method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.mask_type _item_description.description ; The value of _pdbx_phasing_dm.mask_type identifies the type of mask used for density modification ; _item.name '_pdbx_phasing_dm.mask_type' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_pdbx_phasing_dm.mask_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.fom_acentric _item_description.description ; The value of _pdbx_phasing_dm.fom_acentric identifies the figure of merit for acentric data ; _item.name '_pdbx_phasing_dm.fom_acentric' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm.fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.fom_centric _item_description.description ; The value of _pdbx_phasing_dm.fom_centric identifies the figure of merit for acentric data ; _item.name '_pdbx_phasing_dm.fom_centric' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm.fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.fom _item_description.description ; The value of _pdbx_phasing_dm.fom identifies the figure of merit for all the data ; _item.name '_pdbx_phasing_dm.fom' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm.fom' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.reflns_acentric _item_description.description ; The value of _pdbx_phasing_dm.reflns_acentric identifies the number of acentric reflections. ; _item.name '_pdbx_phasing_dm.reflns_acentric' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_dm.reflns_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.reflns_centric _item_description.description ; The value of _pdbx_phasing_dm.reflns_centric identifies the number of centric reflections. ; _item.name '_pdbx_phasing_dm.reflns_centric' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_dm.reflns_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.reflns _item_description.description ; The value of _pdbx_phasing_dm.reflns identifies the number of centric and acentric reflections. ; _item.name '_pdbx_phasing_dm.reflns' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_dm.reflns' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.delta_phi_initial _item_description.description ; The value of _pdbx_phasing_dm.delta_phi_initial identifies phase difference before density modification ; _item.name '_pdbx_phasing_dm.delta_phi_initial' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm.delta_phi_initial' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm.delta_phi_final _item_description.description ; The value of _pdbx_phasing_dm.delta_phi_final identifies phase difference after density modification ; _item.name '_pdbx_phasing_dm.delta_phi_final' _item.category_id pdbx_phasing_dm _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm.delta_phi_final' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### next category, _pdbx_phasing_dm_shell ### save_pdbx_phasing_dm_shell _category.description ; Data items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell. ; _category.id pdbx_phasing_dm_shell _category.mandatory_code no loop_ _category_key.name '_pdbx_phasing_dm_shell.d_res_low' '_pdbx_phasing_dm_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - density modification with shells ; ; loop_ _pdbx_phasing_dm_shell.d_res_low _pdbx_phasing_dm_shell.d_res_high _pdbx_phasing_dm_shell.reflns _pdbx_phasing_dm_shell.fom _pdbx_phasing_dm_shell.delta_phi_final 100.00 7.73 502 0.879 24.7 7.73 6.24 506 0.857 29.2 6.24 5.50 504 0.838 29.2 5.50 5.02 502 0.851 25.3 5.02 4.67 503 0.831 22.7 # ....... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_phasing_dm_shell.d_res_high _item_description.description ; The value of _pdbx_phasing_dm_shell.d_res_high identifies high resolution ; _item.name '_pdbx_phasing_dm_shell.d_res_high' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code yes _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm_shell.d_res_high' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.d_res_low _item_description.description ; The value of _pdbx_phasing_dm_shell.d_res_low identifies low resolution ; _item.name '_pdbx_phasing_dm_shell.d_res_low' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code yes _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm_shell.d_res_low' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.fom_acentric _item_description.description ; The value of _pdbx_phasing_dm_shell.fom_acentric identifies the figure of merit for acentric data with resolution shells ; _item.name '_pdbx_phasing_dm_shell.fom_acentric' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm_shell.fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.fom_centric _item_description.description ; The value of _pdbx_phasing_dm_shell.fom_centric identifies the figure of merit for centric data with resolution shells. ; _item.name '_pdbx_phasing_dm_shell.fom_centric' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm_shell.fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.fom _item_description.description ; The value of _pdbx_phasing_dm_shell.fom identifies the figure of merit for all the data with resolution shells. ; _item.name '_pdbx_phasing_dm_shell.fom' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm_shell.fom' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.reflns_acentric _item_description.description ; The value of _pdbx_phasing_dm_shell.reflns_acentric identifies the number of acentric reflections with resolution shells. ; _item.name '_pdbx_phasing_dm_shell.reflns_acentric' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_dm_shell.reflns_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.reflns_centric _item_description.description ; The value of _pdbx_phasing_dm_shell.reflns_centric identifies the number of centric reflections with resolution shells. ; _item.name '_pdbx_phasing_dm_shell.reflns_centric' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_dm_shell.reflns_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.reflns _item_description.description ; The value of _pdbx_phasing_dm_shell.reflns identifies the number of centric and acentric reflections with resolution shells. ; _item.name '_pdbx_phasing_dm_shell.reflns' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_dm_shell.reflns' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.delta_phi_initial _item_description.description ; The value of _pdbx_phasing_dm_shell.delta_phi_initial identifies phase difference before density modification with resolution shells. ; _item.name '_pdbx_phasing_dm_shell.delta_phi_initial' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm_shell.delta_phi_initial' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_dm_shell.delta_phi_final _item_description.description ; The value of _pdbx_phasing_dm_shell.delta_phi_final identifies phase difference after density modification with resolution shells. ; _item.name '_pdbx_phasing_dm_shell.delta_phi_final' _item.category_id pdbx_phasing_dm_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_dm_shell.delta_phi_final' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_d_res_low _item_description.description ; _phasing_MAD.pdbx_d_res_low records the lowest resolution for MAD phasing. ; _item.name '_phasing_MAD.pdbx_d_res_low' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_d_res_low' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_d_res_high _item_description.description ; _phasing_MAD.pdbx_d_res_high records the highest resolution for MAD phasing. ; _item.name '_phasing_MAD.pdbx_d_res_high' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_d_res_high' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_reflns_acentric _item_description.description ; _phasing_MAD.pdbx_reflns_acentric records the number of acentric reflections for MAD phasing. ; _item.name '_phasing_MAD.pdbx_reflns_acentric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_phasing_MAD.pdbx_reflns_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_reflns_centric _item_description.description ; _phasing_MAD.pdbx_reflns_centric records the number of centric reflections for MAD phasing. ; _item.name '_phasing_MAD.pdbx_reflns_centric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_phasing_MAD.pdbx_reflns_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_reflns _item_description.description ; _phasing_MAD.pdbx_reflns records the number of reflections used for MAD phasing. ; _item.name '_phasing_MAD.pdbx_reflns' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_phasing_MAD.pdbx_reflns' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_fom_acentric _item_description.description ; _phasing_MAD.pdbx_fom_acentric records the figure of merit using acentric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_fom_acentric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_fom_centric _item_description.description ; _phasing_MAD.pdbx_fom_centric records the figure of merit using centric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_fom_centric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_fom _item_description.description ; _phasing_MAD.pdbx_fom records the figure of merit for MAD phasing. ; _item.name '_phasing_MAD.pdbx_fom' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_fom' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_R_cullis_centric _item_description.description ; _phasing_MAD.pdbx_R_cullis_centric records R_cullis using centric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_R_cullis_centric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_R_cullis_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_R_cullis_acentric _item_description.description ; _phasing_MAD.pdbx_R_cullis_acentric records R_cullis using acentric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_R_cullis_acentric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_R_cullis_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_R_cullis _item_description.description ; _phasing_MAD.pdbx_R_cullis records R_cullis for MAD phasing. ; _item.name '_phasing_MAD.pdbx_R_cullis' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_R_cullis' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_R_kraut_centric _item_description.description ; _phasing_MAD.pdbx_R_kraut_centric records R_kraut using centric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_R_kraut_centric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_R_kraut_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_R_kraut_acentric _item_description.description ; _phasing_MAD.pdbx_R_kraut_acentric records R_kraut using acentric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_R_kraut_acentric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_R_kraut_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_R_kraut _item_description.description ; _phasing_MAD.pdbx_R_kraut records R_kraut for MAD phasing. ; _item.name '_phasing_MAD.pdbx_R_kraut' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_R_kraut' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_loc_centric _item_description.description ; _phasing_MAD.pdbx_loc_centric records lack of closure using centric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_loc_centric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_loc_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_loc_acentric _item_description.description ; _phasing_MAD.pdbx_loc_acentric records lack of closure using acentric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_loc_acentric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_loc_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_loc _item_description.description ; _phasing_MAD.pdbx_loc records lack of closure for MAD phasing. ; _item.name '_phasing_MAD.pdbx_loc' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_power_centric _item_description.description ; _phasing_MAD.pdbx_power_centric records phasing power using centric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_power_centric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_power_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_power_acentric _item_description.description ; _phasing_MAD.pdbx_power_acentric records phasing power using acentric data for MAD phasing. ; _item.name '_phasing_MAD.pdbx_power_acentric' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_power_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_power _item_description.description ; _phasing_MAD.pdbx_power records phasing power for MAD phasing. ; _item.name '_phasing_MAD.pdbx_power' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD.pdbx_power' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_number_data_sets _item_description.description ; _phasing_MAD.pdbx_loc records the number of data sets used for MAD phasing. ; _item.name '_phasing_MAD.pdbx_number_data_sets' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_phasing_MAD.pdbx_number_data_sets' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD.pdbx_anom_scat_method _item_description.description ; _phasing_MAD.pdbx_anom_scat_method records the method used to locate anomalous scatterers for MAD phasing. ; _item.name '_phasing_MAD.pdbx_anom_scat_method' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_phasing_MAD.pdbx_anom_scat_method' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## save_pdbx_phasing_MAD_shell _category.description ; Data items in the PDBX_PHASING_MAD_SHELL category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved (note: the values are overall, but broken down into shells of resolution) ; _category.id pdbx_phasing_MAD_shell _category.mandatory_code no loop_ _category_key.name '_pdbx_phasing_MAD_shell.d_res_low' '_pdbx_phasing_MAD_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _pdbx_phasing_MAD_shell.d_res_low _pdbx_phasing_MAD_shell.d_res_high _pdbx_phasing_MAD_shell.reflns_acentric _pdbx_phasing_MAD_shell.fom_acentric _pdbx_phasing_MAD_shell.reflns_centric _pdbx_phasing_MAD_shell.fom_centric 22.60 7.77 64 0.886 23 0.641 7.77 5.67 132 0.863 32 0.642 5.67 4.68 182 0.842 27 0.737 4.68 4.07 209 0.789 24 0.682 4.07 3.65 246 0.772 27 0.633 3.65 3.34 260 0.752 31 0.700 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_phasing_MAD_shell.d_res_low _item_description.description ; _pdbx_phasing_MAD_shell.d_res_low records the lower resolution for the shell. ; _item.name '_pdbx_phasing_MAD_shell.d_res_low' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code yes _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.d_res_low' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.d_res_high _item_description.description ; _pdbx_phasing_MAD_shell.d_res_high records the higher resolution for the shell. ; _item.name '_pdbx_phasing_MAD_shell.d_res_high' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code yes _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.d_res_high' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.reflns_acentric _item_description.description ; _pdbx_phasing_MAD_shell.reflns_acentric records the number of acentric reflections for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.reflns_acentric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.reflns_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.reflns_centric _item_description.description ; _pdbx_phasing_MAD_shell.reflns_centric records the number of centric reflections for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.reflns_centric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_shell.reflns_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.reflns _item_description.description ; _pdbx_phasing_MAD_shell.reflns records the number of reflections used for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.reflns' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_shell.reflns' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.fom_acentric _item_description.description ; _pdbx_phasing_MAD_shell.fom_acentric records the figure of merit using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.fom_acentric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.fom_centric _item_description.description ; _pdbx_phasing_MAD_shell.fom_centric records the figure of merit using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.fom_centric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.fom _item_description.description ; _pdbx_phasing_MAD_shell.fom records the figure of merit for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.fom' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.fom' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.R_cullis_centric _item_description.description ; _pdbx_phasing_MAD_shell.R_cullis_centric records R_cullis using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.R_cullis_centric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_cullis_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.R_cullis_acentric _item_description.description ; _pdbx_phasing_MAD_shell.R_cullis_acentric records R_cullis using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.R_cullis_acentric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_cullis_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.R_cullis _item_description.description ; _pdbx_phasing_MAD_shell.R_cullis records R_cullis for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.R_cullis' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_cullis' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.R_kraut_centric _item_description.description ; _pdbx_phasing_MAD_shell.R_kraut_centric records R_kraut using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.R_kraut_centric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_kraut_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.R_kraut_acentric _item_description.description ; _pdbx_phasing_MAD_shell.r_kraut_acentric records R_kraut using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.R_kraut_acentric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_kraut_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.R_kraut _item_description.description ; _pdbx_phasing_MAD_shell.R_kraut records R_kraut for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.R_kraut' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_kraut' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.loc_centric _item_description.description ; _pdbx_phasing_MAD_shell.loc_centric records lack of closure using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.loc_centric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.loc_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.loc_acentric _item_description.description ; _pdbx_phasing_MAD_shell.loc_acentric records lack of closure using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.loc_acentric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.loc_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.loc _item_description.description ; _pdbx_phasing_MAD_shell.loc records lack of closure for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.loc' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.power_centric _item_description.description ; _pdbx_phasing_MAD_shell.power_centric records phasing powe using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.power_centric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.power_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.power_acentric _item_description.description ; _pdbx_phasing_MAD_shell.power_acentric records phasing powe using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.power_acentric' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.power_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_shell.power _item_description.description ; _pdbx_phasing_MAD_shell.loc records phasing power for MAD phasing. ; _item.name '_pdbx_phasing_MAD_shell.power' _item.category_id pdbx_phasing_MAD_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_shell.power' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### next category, _pdbx_phasing_MAD_set ### save_pdbx_phasing_MAD_set _category.description ; Record details about each phasing set: (Note: the phasing set is different from data set. for example: if there are three data sets, the inflection point (IP), the peak (PK) and the high remote (HR), the combination of the phasing set will be IP_iso, PK_iso (the isomorphous repleacement with HR as 'native'), IP_ano, PK_ano and HR_ano (the anomalous difference with itself). Therefore, there are five set used for phasing. ; _category.id pdbx_phasing_MAD_set _category.mandatory_code no _category_key.name '_pdbx_phasing_MAD_set.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - three wavelengths ; ; loop_ _pdbx_phasing_MAD_set.id _pdbx_phasing_MAD_set.d_res_low _pdbx_phasing_MAD_set.d_res_high _pdbx_phasing_MAD_set.reflns_acentric _pdbx_phasing_MAD_set.reflns_centric _pdbx_phasing_MAD_set.R_cullis_acentric _pdbx_phasing_MAD_set.R_cullis_centric ISO_1 22.60 2.00 5387 471 0.000 0.000 ISO_2 22.60 2.00 5365 469 0.803 0.718 ISO_3 22.60 2.00 5317 460 0.658 0.500 ANO_1 22.60 2.00 5278 0 0.841 0.000 ANO_2 22.60 2.00 5083 0 0.649 0.000 ANO_3 22.60 2.00 5329 0 0.829 0.000 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_phasing_MAD_set.id _item_description.description ; _pdbx_phasing_MAD_set.id records phase set name for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.id' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_pdbx_phasing_MAD_set.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.d_res_low _item_description.description ; _pdbx_phasing_MAD_set.d_res_low records the lowerest resolution for phasing set. ; _item.name '_pdbx_phasing_MAD_set.d_res_low' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.d_res_low' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.d_res_high _item_description.description ; _pdbx_phasing_MAD_set.d_res_high records the highest resolution for the phasing set. ; _item.name '_pdbx_phasing_MAD_set.d_res_high' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.d_res_high' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.number_of_sites _item_description.description ; _pdbx_phasing_MAD_set.number_of_sites records the number of site refined for the phasing set. ; _item.name '_pdbx_phasing_MAD_set.number_of_sites' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_set.number_of_sites' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.reflns_acentric _item_description.description ; _pdbx_phasing_MAD_set.reflns_acentric records the number of acentric reflections for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.reflns_acentric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_set.reflns_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.reflns_centric _item_description.description ; _pdbx_phasing_MAD_set.reflns_centric records the number of centric reflections for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.reflns_centric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_set.reflns_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.reflns _item_description.description ; _pdbx_phasing_MAD_set.reflns records the number of reflections used for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.reflns' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_set.reflns' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.fom_acentric _item_description.description ; _pdbx_phasing_MAD_set.fom_acentric records the figure of merit using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.fom_acentric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.fom_centric _item_description.description ; _pdbx_phasing_MAD_set.fom_centric records the figure of merit using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.fom_centric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.fom _item_description.description ; _pdbx_phasing_MAD_set.fom records the figure of merit for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.fom' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.fom' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.R_cullis_centric _item_description.description ; _pdbx_phasing_MAD_set.R_cullis_centric records R_cullis using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.R_cullis_centric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.R_cullis_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.R_cullis_acentric _item_description.description ; _pdbx_phasing_MAD_set.R_cullis_acentric records R_cullis using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.R_cullis_acentric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.R_cullis_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.R_cullis _item_description.description ; _pdbx_phasing_MAD_set.R_cullis records R_cullis for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.R_cullis' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.R_cullis' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.R_kraut_centric _item_description.description ; _pdbx_phasing_MAD_set.R_kraut_centric records r_kraut using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.R_kraut_centric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.R_kraut_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.R_kraut_acentric _item_description.description ; _pdbx_phasing_MAD_set.r_kraut_acentric records r_kraut using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.R_kraut_acentric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.R_kraut_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.R_kraut _item_description.description ; _pdbx_phasing_MAD_set.R_kraut records R_kraut for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.R_kraut' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.R_kraut' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.loc_centric _item_description.description ; _pdbx_phasing_MAD_set.loc_centric records lack of closure using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.loc_centric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.loc_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.loc_acentric _item_description.description ; _pdbx_phasing_MAD_set.loc_acentric records lack of closure using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.loc_acentric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.loc_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.loc _item_description.description ; _pdbx_phasing_MAD_set.loc records lack of closure for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.loc' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.power_centric _item_description.description ; _pdbx_phasing_MAD_set.power_centric records phasing powe using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.power_centric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.power_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.power_acentric _item_description.description ; _pdbx_phasing_MAD_set.power_acentric records phasing powe using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.power_acentric' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.power_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set.power _item_description.description ; _pdbx_phasing_MAD_set.power records phasing power for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set.power' _item.category_id pdbx_phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set.power' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### next category, _pdbx_phasing_MAD_set_shell ### save_pdbx_phasing_MAD_set_shell _category.description ; The same as category pdbx_phasing_MAD_set, but broken into shells. ; _category.id pdbx_phasing_MAD_set_shell _category.mandatory_code no loop_ _category_key.name '_pdbx_phasing_MAD_set_shell.id' '_pdbx_phasing_MAD_set_shell.d_res_low' '_pdbx_phasing_MAD_set_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - three wavelengths (SHARP example) ; ; loop_ _pdbx_phasing_MAD_set_shell.id _pdbx_phasing_MAD_set_shell.d_res_low _pdbx_phasing_MAD_set_shell.d_res_high _pdbx_phasing_MAD_set_shell.reflns_acentric _pdbx_phasing_MAD_set_shell.reflns_centric _pdbx_phasing_MAD_set_shell.R_cullis_acentric _pdbx_phasing_MAD_set_shell.R_cullis_centric _pdbx_phasing_MAD_set_shell.power_acentric _pdbx_phasing_MAD_set_shell.power_centric ISO_1 22.60 7.77 64 23 0.000 0.000 0.000 0.000 ISO_1 7.77 5.67 130 32 0.000 0.000 0.000 0.000 ISO_1 5.67 4.68 182 27 0.000 0.000 0.000 0.000 ISO_1 4.68 4.07 207 24 0.000 0.000 0.000 0.000 ANO_1 22.60 7.77 62 0 0.610 0.000 1.804 0.000 ANO_1 7.77 5.67 129 0 0.532 0.000 2.382 0.000 ANO_1 5.67 4.68 178 0 0.673 0.000 1.858 0.000 ANO_1 4.68 4.07 204 0 0.755 0.000 1.605 0.000 # ......... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_phasing_MAD_set_shell.id _item_description.description ; _pdbx_phasing_MAD_set_shell.id records phase set name for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.id' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.d_res_low _item_description.description ; _pdbx_phasing_MAD_set_shell.d_res_low records the lowerest resolution for phasing set. ; _item.name '_pdbx_phasing_MAD_set_shell.d_res_low' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code yes _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.d_res_low' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.d_res_high _item_description.description ; _pdbx_phasing_MAD_set_shell.d_res_high records the highest resolution for the phasing set. ; _item.name '_pdbx_phasing_MAD_set_shell.d_res_high' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code yes _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.d_res_high' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.reflns_acentric _item_description.description ; _pdbx_phasing_MAD_set_shell.reflns_acentric records the number of acentric reflections for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.reflns_acentric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.reflns_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.reflns_centric _item_description.description ; _pdbx_phasing_MAD_set_shell.reflns_centric records the number of centric reflections for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.reflns_centric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.reflns_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.reflns _item_description.description ; _pdbx_phasing_MAD_set_shell.reflns records the number of reflections used for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.reflns' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.reflns' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.fom_acentric _item_description.description ; _pdbx_phasing_MAD_set_shell.fom_acentric records the figure of merit using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.fom_acentric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.fom_centric _item_description.description ; _pdbx_phasing_MAD_set_shell.fom_centric records the figure of merit using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.fom_centric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.fom _item_description.description ; _pdbx_phasing_MAD_set_shell.fom records the figure of merit for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.fom' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.fom' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.R_cullis_centric _item_description.description ; _pdbx_phasing_MAD_set_shell.R_cullis_centric records R_cullis using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.R_cullis_centric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_cullis_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.R_cullis_acentric _item_description.description ; _pdbx_phasing_MAD_set_shell.R_cullis_acentric records R_cullis using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.R_cullis_acentric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_cullis_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.R_cullis _item_description.description ; _pdbx_phasing_MAD_set_shell.R_cullis records R_cullis for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.R_cullis' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_cullis' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.R_kraut_centric _item_description.description ; _pdbx_phasing_MAD_set_shell.R_kraut_centric records R_kraut using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.R_kraut_centric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_kraut_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.R_kraut_acentric _item_description.description ; _pdbx_phasing_MAD_set_shell.R_kraut_acentric records R_kraut using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.R_kraut_acentric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_kraut_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.R_kraut _item_description.description ; _pdbx_phasing_MAD_set_shell.R_kraut records R_kraut for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.R_kraut' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_kraut' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.loc_centric _item_description.description ; _pdbx_phasing_MAD_set_shell.loc_centric records lack of closure using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.loc_centric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.loc_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.loc_acentric _item_description.description ; _pdbx_phasing_MAD_set_shell.loc_acentric records lack of closure using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.loc_acentric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.loc_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.loc _item_description.description ; _pdbx_phasing_MAD_set_shell.loc records lack of closure for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.loc' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.power_centric _item_description.description ; _pdbx_phasing_MAD_set_shell.power_centric records phasing power using centric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.power_centric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.power_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.power_acentric _item_description.description ; _pdbx_phasing_MAD_set_shell.power_acentric records phasing power using acentric data for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.power_acentric' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.power_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_shell.power _item_description.description ; _pdbx_phasing_MAD_set_shell.power records phasing power for MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_shell.power' _item.category_id pdbx_phasing_MAD_set_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.power' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### next category, _pdbx_phasing_MAD_set_site ### save_pdbx_phasing_MAD_set_site _category.description ; record the details (coordinates etc.) of anomalous scatters. ; _category.id pdbx_phasing_MAD_set_site _category.mandatory_code no _category_key.name '_pdbx_phasing_MAD_set_site.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - anomalous scatters is Se ; ; loop_ _pdbx_phasing_MAD_set_site.id _pdbx_phasing_MAD_set_site.atom_type_symbol _pdbx_phasing_MAD_set_site.Cartn_x _pdbx_phasing_MAD_set_site.Cartn_y _pdbx_phasing_MAD_set_site.Cartn_z _pdbx_phasing_MAD_set_site.B_iso _pdbx_phasing_MAD_set_site.Occupancy 1 SE 25.9407 -0.103471 17.4094 15.2561 1 2 SE 30.6534 6.62359 9.93063 12.9102 1 3 SE -3.26506 15.5546 53.9529 30.5239 1 # ....... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_phasing_MAD_set_site.id _item_description.description ; _pdbx_phasing_MAD_set_site.id records the number of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.id' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.atom_type_symbol _item_description.description ; _pdbx_phasing_MAD_set_site.atom_type_symbol records the name of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.atom_type_symbol' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.atom_type_symbol' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.Cartn_x _item_description.description ; _pdbx_phasing_MAD_set_site.Cartn_x records the X Cartesian coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.Cartn_x' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_x' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.Cartn_y _item_description.description ; _pdbx_phasing_MAD_set_site.Cartn_y records the Y Cartesian coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.Cartn_y' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_y' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.Cartn_z _item_description.description ; _pdbx_phasing_MAD_set_site.Cartn_z records the Z Cartesian coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.Cartn_z' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_z' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.Cartn_x_esd _item_description.description ; _pdbx_phasing_MAD_set_site.Cartn_x_esd records the estimated standard deviation X Cartesian coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.Cartn_x_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_x_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.Cartn_y_esd _item_description.description ; _pdbx_phasing_MAD_set_site.Cartn_y_esd records the estimated standard deviation Y Cartesian coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.Cartn_y_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_y_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.Cartn_z_esd _item_description.description ; _pdbx_phasing_MAD_set_site.Cartn_z_esd records the estimated standard deviation Z Cartesian coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.Cartn_z_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_z_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.fract_x _item_description.description ; _pdbx_phasing_MAD_set_site.fract_x records the X fractional coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.fract_x' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_x' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.fract_y _item_description.description ; _pdbx_phasing_MAD_set_site.fract_y records the Y fractional coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.fract_y' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_y' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.fract_z _item_description.description ; _pdbx_phasing_MAD_set_site.fract_z records the Z fractional coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.fract_z' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_z' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.fract_x_esd _item_description.description ; _pdbx_phasing_MAD_set_site.fract_x_esd records the estimated standard deviation X fractional coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.fract_x_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_x_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.fract_y_esd _item_description.description ; _pdbx_phasing_MAD_set_site.fract_y_esd records the estimated standard deviation Y fractional coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.fract_y_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_y_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.fract_z_esd _item_description.description ; _pdbx_phasing_MAD_set_site.fract_z_esd records the estimated standard deviation Z fractional coordinate of site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.fract_z_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_z_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.b_iso _item_description.description ; _pdbx_phasing_MAD_set_site.b_iso records isotropic temperature factor parameterthe for the site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.b_iso' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.b_iso' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.b_iso_esd _item_description.description ; _pdbx_phasing_MAD_set_site.b_iso_esd records estimated standard deviation of isotropic temperature factor parameterthe for the site obtained from MAD phasing. ; _item.name '_pdbx_phasing_MAD_set_site.b_iso_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.b_iso_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.occupancy _item_description.description ; _pdbx_phasing_MAD_set_site.occupancy records the fraction of the atom type presented at this site. ; _item.name '_pdbx_phasing_MAD_set_site.occupancy' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.occupancy' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.occupancy_esd _item_description.description ; _pdbx_phasing_MAD_set_site.occupancy_esd records estimated standard deviation of the fraction of the atom type presented at this site. ; _item.name '_pdbx_phasing_MAD_set_site.occupancy_esd' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.occupancy_esd' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ### new items for _phasing_MAD_set ### save__phasing_MAD_set.pdbx_atom_type _item_description.description ; record the type of heavy atoms which produce anomolous singal. ; _item.name '_phasing_MAD_set.pdbx_atom_type' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_phasing_MAD_set.pdbx_atom_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD_set.pdbx_f_prime_refined _item_description.description ; record the refined f_prime (not from experiment). ; _item.name '_phasing_MAD_set.pdbx_f_prime_refined' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD_set.pdbx_f_prime_refined' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MAD_set.pdbx_f_double_prime_refined _item_description.description ; record the refined f_double_prime (not from experiment). ; _item.name '_phasing_MAD_set.pdbx_f_double_prime_refined' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MAD_set.pdbx_f_double_prime_refined' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### new items for _pdbx_phasing_MAD_set_site ### save__pdbx_phasing_MAD_set_site.set_id _item_description.description ; record the phasing set. ; _item.name '_pdbx_phasing_MAD_set_site.set_id' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.set_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MAD_set_site.occupancy_iso _item_description.description ; The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given atom site. ; _item.name '_pdbx_phasing_MAD_set_site.occupancy_iso' _item.category_id pdbx_phasing_MAD_set_site _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MAD_set_site.occupancy_iso' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### new items for _refine_ls_restr_ncs ### save__refine_ls_restr_ncs.pdbx_type _item_description.description ; record the type of NCS restraint. (for example: tight positional) ; _item.name '_refine_ls_restr_ncs.pdbx_type' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_type' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_ls_restr_ncs.pdbx_asym_id _item_description.description ; record the chain ID. ; _item.name '_refine_ls_restr_ncs.pdbx_asym_id' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_asym_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_ls_restr_ncs.pdbx_number _item_description.description ; record the residue number . ; _item.name '_refine_ls_restr_ncs.pdbx_number' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_number' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_ls_restr_ncs.pdbx_rms _item_description.description ; record the standard divation between one segment to another ; _item.name '_refine_ls_restr_ncs.pdbx_rms' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_rms' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__refine_ls_restr_ncs.pdbx_weight _item_description.description ; record the weight used for NCS restraint. ; _item.name '_refine_ls_restr_ncs.pdbx_weight' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_weight' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### new items for _struct_ncs_dom_lim ### save__struct_ncs_dom_lim.pdbx_component_id _item_description.description ; record the number of component used for NCS. ; _item.name '_struct_ncs_dom_lim.pdbx_component_id' _item.category_id struct_ncs_dom_lim _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_struct_ncs_dom_lim.pdbx_component_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ncs_dom_lim.pdbx_refine_code _item_description.description ; record the refinement code number (from CCP4.) ; _item.name '_struct_ncs_dom_lim.pdbx_refine_code' _item.category_id struct_ncs_dom_lim _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_struct_ncs_dom_lim.pdbx_refine_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### new items for _refine_analyze ### save__refine_analyze.pdbx_Luzzati_d_res_high_obs _item_description.description ; record the high resolution for calculating Luzzati statistics. ; _item.name '_refine_analyze.pdbx_Luzzati_d_res_high_obs' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_refine_analyze.pdbx_Luzzati_d_res_high_obs' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ #------------------------------- ### new items for _phasing_MIR_shell ### save__phasing_MIR.pdbx_number_derivatives _item_description.description ; The number of derivatives used in this phasing experiment. ; _item.name '_phasing_MIR.pdbx_number_derivatives' _item.category_id phasing_MIR _item.mandatory_code no _item_type.code int save_ save__phasing_MIR_shell.pdbx_loc_centric _item_description.description ; record lack of closure from centric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_loc_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_loc_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_shell.pdbx_loc_acentric _item_description.description ; record lack of closure from acentric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_loc_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_loc_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_shell.pdbx_power_centric _item_description.description ; record phasing power from centric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_power_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_power_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_shell.pdbx_power_acentric _item_description.description ; record phasing power from acentric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_power_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_power_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_shell.pdbx_R_kraut_centric _item_description.description ; record R_Kraut from from centric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_R_kraut_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_kraut_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_shell.pdbx_R_kraut_acentric _item_description.description ; record R_kraut from from acentric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_R_kraut_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_kraut_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_shell.pdbx_R_cullis_centric _item_description.description ; record R_Cullis from from centric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_R_cullis_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_cullis_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_shell.pdbx_R_cullis_acentric _item_description.description ; record R_Cullis from from acentric reflection for each shell. ; _item.name '_phasing_MIR_shell.pdbx_R_cullis_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_cullis_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### new items for _phasing_MIR_der ### save__phasing_MIR_der.pdbx_R_kraut_centric _item_description.description ; record R_kraut obtained from centric data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_R_kraut_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_R_kraut_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_R_kraut_acentric _item_description.description ; record R_kraut obtained from acentric data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_R_kraut_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_R_kraut_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_R_kraut _item_description.description ; record R_kraut obtained from all data data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_R_kraut' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_R_kraut' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_loc_centric _item_description.description ; record lack of closure obtained from centric data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_loc_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_loc_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_loc_acentric _item_description.description ; record lack of closure obtained from acentric data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_loc_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_loc_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_loc _item_description.description ; record lack of closure obtained from all data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_loc' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_loc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_fom_centric _item_description.description ; record figure of merit obtained from centric data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_fom_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_fom_acentric _item_description.description ; record figure of merit obtained from acentric data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_fom_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_fom _item_description.description ; record figure of merit obtained from all data for each derivative. ; _item.name '_phasing_MIR_der.pdbx_fom' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_fom' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_power _item_description.description ; record phasing power for each derivative. ; _item.name '_phasing_MIR_der.pdbx_power' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_power' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_R_cullis _item_description.description ; record R_cullis for each derivative. ; _item.name '_phasing_MIR_der.pdbx_R_cullis' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der.pdbx_R_cullis' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der.pdbx_reflns _item_description.description ; record number of reflections used for each derivative. ; _item.name '_phasing_MIR_der.pdbx_reflns' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_phasing_MIR_der.pdbx_reflns' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ### new items for _phasing_MIR_der_shell ### save__phasing_MIR_der_shell.pdbx_R_cullis_centric _item_description.description ; record R Cullis obtained from centric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_R_cullis_centric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_cullis_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_R_cullis_acentric _item_description.description ; record R Cullis obtained from acentric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_R_cullis_acentric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_cullis_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_R_kraut_centric _item_description.description ; record R Kraut obtained from centric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_R_kraut_centric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_kraut_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_R_kraut_acentric _item_description.description ; record R Kraut obtained from acentric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_R_kraut_acentric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_kraut_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_loc_centric _item_description.description ; record lack of closure obtained from centric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_loc_centric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_loc_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_loc_acentric _item_description.description ; record lack of closure obtained from acentric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_loc_acentric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_loc_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_power_centric _item_description.description ; record phasing power obtained from centric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_power_centric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_power_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_power_acentric _item_description.description ; record phasing power obtained from acentric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_power_acentric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_power_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_fom_centric _item_description.description ; record figure of merit obtained from centric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_fom_centric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_fom_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_fom_acentric _item_description.description ; record figure of merit obtained from acentric data for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_fom_acentric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_fom_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_reflns_centric _item_description.description ; record number of centric reflections used for phasing for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_reflns_centric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_reflns_centric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__phasing_MIR_der_shell.pdbx_reflns_acentric _item_description.description ; record number of acentric reflections used for phasing for each derivative, but broken into resolution shells ; _item.name '_phasing_MIR_der_shell.pdbx_reflns_acentric' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_reflns_acentric' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ## ### category, _pdbx_phasing_MR save_pdbx_phasing_MR _category.description ; Data items in the PDBX_PHASING_MR category record details about molecular replacement. ; _category.id pdbx_phasing_MR _category.mandatory_code no _category_key.name '_pdbx_phasing_MR.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - molecular replacement example from program CNS. ; ; _pdbx_phasing_MR.entry_id ABC001 _pdbx_phasing_MR.method_rotation 'real-space rotation search' _pdbx_phasing_MR.d_res_high_rotation 3.8 _pdbx_phasing_MR.d_res_low_rotation 13.0 _pdbx_phasing_MR.sigma_F_rotation 1.0 _pdbx_phasing_MR.reflns_percent_rotation 97.8 _pdbx_phasing_MR.method_translation 'gerneral using PC-refinement= e2e2' _pdbx_phasing_MR.d_res_high_translation 4.0 _pdbx_phasing_MR.d_res_low_translation 15.0 _pdbx_phasing_MR.sigma_F_translation 0 _pdbx_phasing_MR.reflns_percent_translation 97.7 _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc 0.586 _pdbx_phasing_MR.packing 0.3086 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_phasing_MR.entry_id _item_description.description ; The value of _pdbx_phasing_MR.entry_id identifies the data block. ; _item.name '_pdbx_phasing_MR.entry_id' _item.category_id pdbx_phasing_MR _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_pdbx_phasing_MR.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.method_rotation _item_description.description ; The value of _pdbx_phasing_MR.method_rotation identifies the method used for rotation search. For example, the rotation method may be realspace, fastdirect, or direct. . ; _item.name '_pdbx_phasing_MR.method_rotation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_pdbx_phasing_MR.method_rotation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.d_res_high_rotation _item_description.description ; The value of _pdbx_phasing_MR.d_res_high_rotation identifies the highest resolution used for rotation search. ; _item.name '_pdbx_phasing_MR.d_res_high_rotation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.d_res_high_rotation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.d_res_low_rotation _item_description.description ; The value of _pdbx_phasing_MR.d_res_low_rotation identifies the lowest resolution used for rotation search. ; _item.name '_pdbx_phasing_MR.d_res_low_rotation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.d_res_low_rotation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.sigma_F_rotation _item_description.description ; The value of _pdbx_phasing_MR.sigma_F_rotation identifies the sigma cut off of structure factor used for rotation search. ; _item.name '_pdbx_phasing_MR.sigma_F_rotation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.sigma_F_rotation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.sigma_I_rotation _item_description.description ; The value of _pdbx_phasing_MR.sigma_I_rotation identifies the sigma cut off of intensity used for rotation search. ; _item.name '_pdbx_phasing_MR.sigma_I_rotation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.sigma_I_rotation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.reflns_percent_rotation _item_description.description ; The value of _pdbx_phasing_MR.reflns_percent_rotation identifies the completness of data used for rotation search. ; _item.name '_pdbx_phasing_MR.reflns_percent_rotation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.reflns_percent_rotation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.method_translation _item_description.description ; The value of _pdbx_phasing_MR.method_translation identifies the method used for translation search. For example in CNS, the translation method may be "general" or "phased" with PC refinement target using "fastf2f2" "e2e2" "e1e1" "f2f2" "f1f1" "residual" "vector". . ; _item.name '_pdbx_phasing_MR.method_translation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code line _item_aliases.alias_name '_pdbx_phasing_MR.method_translation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.d_res_high_translation _item_description.description ; The value of _pdbx_phasing_MR.d_res_high_translation identifies the highest resolution used for translation search. ; _item.name '_pdbx_phasing_MR.d_res_high_translation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.d_res_high_translation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.d_res_low_translation _item_description.description ; The value of _pdbx_phasing_MR.d_res_low_translation identifies the lowest resolution used for translation search. ; _item.name '_pdbx_phasing_MR.d_res_low_translation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.d_res_low_translation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.sigma_F_translation _item_description.description ; The value of _pdbx_phasing_MR.sigma_F_translation identifies the sigma cut off of structure factor used for translation search. ; _item.name '_pdbx_phasing_MR.sigma_F_translation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.sigma_F_translation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.sigma_I_translation _item_description.description ; The value of _pdbx_phasing_MR.sigma_I_translation identifies the sigma cut off of intensity used for translation search. ; _item.name '_pdbx_phasing_MR.sigma_I_translation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.sigma_I_translation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.reflns_percent_translation _item_description.description ; The value of _pdbx_phasing_MR.reflns_percent_translation identifies the completness of data used for translation search. ; _item.name '_pdbx_phasing_MR.reflns_percent_translation' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.reflns_percent_translation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.correlation_coeff_Io_to_Ic _item_description.description ; The value of _pdbx_phasing_MR.correlation_coeff_Io_to_Ic identifies the correlation between the observed and the calculated intensity (~|F|^2) after rotation and translation. ; _item.name '_pdbx_phasing_MR.correlation_coeff_Io_to_Ic' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.correlation_coeff_Io_to_Ic' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.correlation_coeff_Fo_to_Fc _item_description.description ; The value of _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc identifies the correlation between the observed and the calculated structure factor after rotation and translation. ; _item.name '_pdbx_phasing_MR.correlation_coeff_Fo_to_Fc' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.correlation_coeff_Fo_to_Fc' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.R_factor _item_description.description ; The value of _pdbx_phasing_MR.R_factor identifies the R factor (defined as uasual) after rotation and translation. ; _item.name '_pdbx_phasing_MR.R_factor' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.R_factor' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.R_rigid_body _item_description.description ; The value of _pdbx_phasing_MR.R_rigid_body identifies the R factor for rigid body refinement after rotation and translation.(In general, rigid body refinement has to be carried out after molecular replacement. ; _item.name '_pdbx_phasing_MR.R_rigid_body' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.R_rigid_body' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.packing _item_description.description ; The value of _pdbx_phasing_MR.packing identifies the packing of search model in the unit cell. Too many crystallographic contacts may indicate a bad search. ; _item.name '_pdbx_phasing_MR.packing' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code float _item_aliases.alias_name '_pdbx_phasing_MR.packing' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.model_details _item_description.description ; The value of _pdbx_phasing_MR.model_details records the details of model used. For example, the original model can be truncated by deleting side chains, doubtful parts, using the monomer if the original model was an oligomer. The search model may be one domain of a large molecule. What is the pdb IDs. ; _item.name '_pdbx_phasing_MR.model_details' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code text _item_aliases.alias_name '_pdbx_phasing_MR.model_details' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_phasing_MR.native_set_id _item_description.description ; The data set that was treated as the native in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_pdbx_phasing_MR.native_set_id' _item.category_id pdbx_phasing_MR _item.mandatory_code no _item_type.code line _item_linked.child_name '_pdbx_phasing_MR.native_set_id' _item_linked.parent_name '_phasing_set.id' save_ save__phasing_set.pdbx_temp_details _item_description.description ; The value of _phasing_set.pdbx_temp_details describes any special details about the data collection temperature for this phasing data set. ; _item.name '_phasing_set.pdbx_temp_details' _item.category_id phasing_set _item.mandatory_code no _item_type.code text save_ save__phasing_set.pdbx_d_res_high _item_description.description ; The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. ; _item.name '_phasing_set.pdbx_d_res_high' _item.category_id phasing_set _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_set.pdbx_d_res_low _item_description.description ; The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. ; _item.name '_phasing_set.pdbx_d_res_low' _item.category_id phasing_set _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refln.pdbx_I_plus _item_description.description ; The intensity of the I(h,k,l) partner of the Friedel pair. ; _item.name '_refln.pdbx_I_plus' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_I_minus _item_description.description ; The intensity of the I(-h,-k,-l) partner of the Friedel pair. ; _item.name '_refln.pdbx_I_minus' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_F_plus _item_description.description ; The structure factor F(h,k,l) of the Friedel pair. ; _item.name '_refln.pdbx_F_plus' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_F_minus _item_description.description ; The structure factor F(-h,-k,-l) of the Friedel pair. ; _item.name '_refln.pdbx_F_minus' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_I_plus_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the intensity I(h,k,l) partner of the Friedel pair. ; _item.name '_refln.pdbx_I_plus_sigma' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_I_minus_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the intensity I(-h,-k,-l) partner of the Friedel pair. ; _item.name '_refln.pdbx_I_minus_sigma' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_F_minus_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the structure factor F(-h,-k,-l) of the Friedel pair. ; _item.name '_refln.pdbx_F_minus_sigma' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_F_plus_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the structure factor F(h,k,l) of the Friedel pair. ; _item.name '_refln.pdbx_F_plus_sigma' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_HL_A_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_refln.pdbx_HL_A_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_HL_B_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_refln.pdbx_HL_B_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_HL_C_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_refln.pdbx_HL_C_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ save__refln.pdbx_HL_D_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_refln.pdbx_HL_D_iso' _item.category_id refln _item.mandatory_code no _item_type.code float save_ ### EOF mmcif_pdbx-def-5.dic ########################################################################### # # File: mmcif_pdbx-def-6.dic # # PDB Exchange Data Dictionary # # This data dictionary contains definitions used by wwPDB for data exchange # and data processing. # # Definition Section 6 # # ########################################################################### save__entity.pdbx_target_id _item_description.description ; The value of _entity.target_id points to a TARGETDB target idenitifier from which this entity was generated. ; _item.name '_entity.pdbx_target_id' _item.category_id entity _item.mandatory_code no _item_type.code code save_ save_pdbx_entity_prod_protocol _category.description ; This category contains descriptive protocols for the production of this entity. ; _category.id pdbx_entity_prod_protocol _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_prod_protocol.entry_id' '_pdbx_entity_prod_protocol.entity_id' '_pdbx_entity_prod_protocol.protocol_type' save_ save__pdbx_entity_prod_protocol.entry_id _item_description.description ; The value of _pdbx_entity_prod_protocol.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. ; _item.name '_pdbx_entity_prod_protocol.entry_id' _item.category_id pdbx_entity_prod_protocol _item.mandatory_code yes _item_type.code code _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_prod_protocol.entry_id' save_ save__pdbx_entity_prod_protocol.entity_id _item_description.description ; The value of _pdbx_entity_prod_protocol.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_pdbx_entity_prod_protocol.entity_id' _item.category_id pdbx_entity_prod_protocol _item.mandatory_code yes _item_type.code code _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_prod_protocol.entity_id' save_ save__pdbx_entity_prod_protocol.protocol _item_description.description ; The protocol description associated with the protocol_type employed in the production of this entity. ; _item.name '_pdbx_entity_prod_protocol.protocol' _item.category_id pdbx_entity_prod_protocol _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_prod_protocol.protocol_type _item_description.description ; The one of a set of protocol types associated with the production of this entity. ; _item.name '_pdbx_entity_prod_protocol.protocol_type' _item.category_id pdbx_entity_prod_protocol _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value "selection" "PCR" "cloning" "expression" "growth" "purification" "NMR" "other" save_ #################### ## ENTITY_SRC_GEN ## #################### save__entity_src_gen.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_src_gen.entity_id' _item.mandatory_code yes save_ save__entity_src_gen.host_org_common_name _item_description.description ; The common name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item be derived from _entity_src_gen_express.host_org_common_name or via _entity_src_gen_express.host_org_tax_id ; _item.name '_entity_src_gen.host_org_common_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'yeast' 'bacteria' save_ save__entity_src_gen.host_org_details _item_description.description ; A description of special aspects of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would derived from _entity_src_gen_express.host_org_details ; _item.name '_entity_src_gen.host_org_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.host_org_strain _item_description.description ; The strain of the organism in which the entity was expressed. Where full details of the protein production are available it would be expected that this item be derived from _entity_src_gen_express.host_org_strain or via _entity_src_gen_express.host_org_tax_id ; _item.name '_entity_src_gen.host_org_strain' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__entity_src_gen.plasmid_details _item_description.description ; A description of special aspects of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from _pdbx_construct.details of the construct pointed to from _entity_src_gen_express.plasmid_id. ; _item.name '_entity_src_gen.plasmid_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.plasmid_name _item_description.description ; The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from _pdbx_construct.name of the construct pointed to from _entity_src_gen_express.plasmid_id. ; _item.name '_entity_src_gen.plasmid_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'pET3C' 'pT123sab' save_ save__entity_src_gen.pdbx_host_org_variant _item_description.description ; Variant of the organism used as the expression system. Where full details of the protein production are available it would be expected that this item be derived from entity_src_gen_express.host_org_variant or via _entity_src_gen_express.host_org_tax_id ; _item.name '_entity_src_gen.pdbx_host_org_variant' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'TRP-LAC' 'LAMBDA DE3' save_ save__entity_src_gen.pdbx_host_org_cell_line _item_description.description ; A specific line of cells used as the expression system. Where full details of the protein production are available it would be expected that this item would be derived from entity_src_gen_express.host_org_cell_line ; _item.name '_entity_src_gen.pdbx_host_org_cell_line' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case 'HELA' save_ save__entity_src_gen.pdbx_host_org_atcc _item_description.description ; Americal Tissue Culture Collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_culture_collection ; _item.name '_entity_src_gen.pdbx_host_org_atcc' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.pdbx_host_org_culture_collection _item_description.description ; Culture collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived somehwere, but exactly where is not clear. ; _item.name '_entity_src_gen.pdbx_host_org_culture_collection' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.pdbx_host_org_cell _item_description.description ; Cell type from which the gene is derived. Where entity.target_id is provided this should be derived from details of the target. ; _item.name '_entity_src_gen.pdbx_host_org_cell' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text _item_examples.case ENDOTHELIAL save_ save__entity_src_gen.pdbx_host_org_scientific_name _item_description.description ; The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_scientific_name or via _entity_src_gen_express.host_org_tax_id ; _item.name '_entity_src_gen.pdbx_host_org_scientific_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'ESCHERICHIA COLI' 'SACCHAROMYCES CEREVISIAE' save_ save__entity_src_gen.pdbx_host_org_tissue _item_description.description ; The specific tissue which expressed the molecule. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_tissue ; _item.name '_entity_src_gen.pdbx_host_org_tissue' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' save_ save__entity_src_gen.pdbx_host_org_vector _item_description.description ; Identifies the vector used. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_clone.vector_name. ; _item.name '_entity_src_gen.pdbx_host_org_vector' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'PBIT36' 'PET15B' 'PUC18' save_ save__entity_src_gen.pdbx_host_org_vector_type _item_description.description ; Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.vector_type. ; _item.name '_entity_src_gen.pdbx_host_org_vector_type' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'COSMID' 'PLASMID' save_ save__entity_src_gen.expression_system_id _item_description.description ; A unique identifier for the expression system. This should be extracted from a local list of expression systems. ; _item.name '_entity_src_gen.expression_system_id' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code uline save_ save__entity_src_gen.gene_src_dev_stage _item_description.description ; A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active. ; _item.name '_entity_src_gen.gene_src_dev_stage' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.start_construct_id _item_description.description ; A pointer to _pdbx_construct.id in the PDBX_CONSTRUCT category. The indentified sequence is the initial construct. ; _item.name '_entity_src_gen.start_construct_id' _item.category_id entity_src_gen _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_entity_src_gen.start_construct_id' save_ ############################# # ENTITY_SRC_GEN_PROD_OTHER # ############################# # # _pdbx_entity_src_gen_prod_other.entry_id # _pdbx_entity_src_gen_prod_other.entity_id # _pdbx_entity_src_gen_prod_other.step_id # _pdbx_entity_src_gen_prod_other.next_step_id # _pdbx_entity_src_gen_prod_other.end_construct_id # _pdbx_entity_src_gen_prod_other.process_name # _pdbx_entity_src_gen_prod_other.date # _pdbx_entity_src_gen_prod_other.robot_id # _pdbx_entity_src_gen_prod_other.details # save_pdbx_entity_src_gen_prod_other _category.description ; This category contains details for process steps that are not explicitly catered for elsewhere. It provides some basic details as well as placeholders for a list of parameters and values (the category PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER). Note that processes that have been modelled explicitly should not be represented using this category. ; _category.id pdbx_entity_src_gen_prod_other _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_prod_other.entry_id' '_pdbx_entity_src_gen_prod_other.entity_id' '_pdbx_entity_src_gen_prod_other.step_id' save_ save__pdbx_entity_src_gen_prod_other.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_other.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_prod_other.entry_id' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_other.entry_id' save_ save__pdbx_entity_src_gen_prod_other.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_other.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_prod_other.entity_id' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_other.entity_id' save_ save__pdbx_entity_src_gen_prod_other.step_id _item_description.description ; This item is the unique identifier for this process step. ; _item.name '_pdbx_entity_src_gen_prod_other.step_id' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_prod_other.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_prod_other.next_step_id' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_prod_other.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the product of the process step. ; _item.name '_pdbx_entity_src_gen_prod_other.end_construct_id' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_other.end_construct_id' save_ save__pdbx_entity_src_gen_prod_other.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The referenced robot is the robot responsible for the process step ; _item.name '_pdbx_entity_src_gen_prod_other.robot_id' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_other.robot_id' save_ save__pdbx_entity_src_gen_prod_other.date _item_description.description ; The date of this process step. ; _item.name '_pdbx_entity_src_gen_prod_other.date' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_prod_other.process_name _item_description.description ; Name of this process step. ; _item.name '_pdbx_entity_src_gen_prod_other.process_name' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_prod_other.details _item_description.description ; Additional details of this process step. ; _item.name '_pdbx_entity_src_gen_prod_other.details' _item.category_id pdbx_entity_src_gen_prod_other _item.mandatory_code no _item_type.code text save_ ############################################ # PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER # ############################################ # # _pdbx_entity_src_gen_prod_other_parameter.entry_id # _pdbx_entity_src_gen_prod_other_parameter.entity_id # _pdbx_entity_src_gen_prod_other_parameter.step_id # _pdbx_entity_src_gen_prod_other_parameter.name # _pdbx_entity_src_gen_prod_other_parameter.value # save_pdbx_entity_src_gen_prod_other_parameter _category.description ; This category contains parameters and values required to capture information about a particular process step ; _category.id pdbx_entity_src_gen_prod_other_parameter _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_prod_other_parameter.entry_id' '_pdbx_entity_src_gen_prod_other_parameter.entity_id' '_pdbx_entity_src_gen_prod_other_parameter.step_id' '_pdbx_entity_src_gen_prod_other_parameter.parameter' save_ save__pdbx_entity_src_gen_prod_other_parameter.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_other_parameter.entry_id is a pointer to _pdbx_entity_src_gen_prod_other.entry.id ; _item.name '_pdbx_entity_src_gen_prod_other_parameter.entry_id' _item.category_id pdbx_entity_src_gen_prod_other_parameter _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_prod_other.entry_id' _item_linked.child_name '_pdbx_entity_src_gen_prod_other_parameter.entry_id' save_ save__pdbx_entity_src_gen_prod_other_parameter.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_other_parameter.entity_id is a pointer to _pdbx_entity_src_gen_prod_other.entity_id ; _item.name '_pdbx_entity_src_gen_prod_other_parameter.entity_id' _item.category_id pdbx_entity_src_gen_prod_other_parameter _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_prod_other.entity_id' _item_linked.child_name '_pdbx_entity_src_gen_prod_other_parameter.entity_id' save_ save__pdbx_entity_src_gen_prod_other_parameter.step_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_prod_other.step_id ; _item.name '_pdbx_entity_src_gen_prod_other_parameter.step_id' _item.category_id pdbx_entity_src_gen_prod_other_parameter _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_prod_other.step_id' _item_linked.child_name '_pdbx_entity_src_gen_prod_other_parameter.step_id' save_ save__pdbx_entity_src_gen_prod_other_parameter.parameter _item_description.description ; The name of the parameter associated with the process step ; _item.name '_pdbx_entity_src_gen_prod_other_parameter.parameter' _item.category_id pdbx_entity_src_gen_prod_other_parameter _item.mandatory_code yes _item_type.code line save_ save__pdbx_entity_src_gen_prod_other_parameter.value _item_description.description ; The value of the parameter ; _item.name '_pdbx_entity_src_gen_prod_other_parameter.value' _item.category_id pdbx_entity_src_gen_prod_other_parameter _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_prod_other_parameter.details _item_description.description ; Additional details about the parameter ; _item.name '_pdbx_entity_src_gen_prod_other_parameter.details' _item.category_id pdbx_entity_src_gen_prod_other_parameter _item.mandatory_code yes _item_type.code text save_ ################################ # PDBX_ENTITY_SRC_GEN_PROD_PCR # ################################ # # _pdbx_entity_src_gen_prod_pcr.entry_id # _pdbx_entity_src_gen_prod_pcr.entity_id # _pdbx_entity_src_gen_prod_pcr.step_id # _pdbx_entity_src_gen_prod_pcr.next_step_id # _pdbx_entity_src_gen_prod_pcr.end_construct_id # _pdbx_entity_src_gen_prod_pcr.forward_primer_id # _pdbx_entity_src_gen_prod_pcr.reverse_primer_id # _pdbx_entity_src_gen_prod_pcr.reaction_details # _pdbx_entity_src_gen_prod_pcr.purification_details # _pdbx_entity_src_gen_prod_pcr.date # _pdbx_entity_src_gen_prod_pcr.robot_id # # _pdbx_entity_src_gen_prod_pcr.summary # save_pdbx_entity_src_gen_prod_pcr _category.description ; This category contains details for the PCR steps used in the overall protein production process. The PCR is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step. ; _category.id pdbx_entity_src_gen_prod_pcr _category.mandatory_code no loop_ _category_key.name '_pdbx_entity_src_gen_prod_pcr.entry_id' '_pdbx_entity_src_gen_prod_pcr.entity_id' '_pdbx_entity_src_gen_prod_pcr.step_id' loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example ; ; _pdbx_entity_src_gen_prod_pcr.entry_id 111000111 _pdbx_entity_src_gen_prod_pcr.entity_id 222000111 _pdbx_entity_src_gen_prod_pcr.step_id 1 _pdbx_entity_src_gen_prod_pcr.next_step_id 2 _pdbx_entity_src_gen_prod_pcr.end_construct_id 440050000111 _pdbx_entity_src_gen_prod_pcr.robot_id 5 _pdbx_entity_src_gen_prod_pcr.date '2002-07-12:15:13' _pdbx_entity_src_gen_prod_pcr.forward_primer_id 2 _pdbx_entity_src_gen_prod_pcr.reverse_primer_id 3 _pdbx_entity_src_gen_prod_pcr.reaction_details ; Annealing temperature = 70 C Annealing time = 60 s Extending temperature = 74 C Extending time = 120 s Melting temperature = 95 C Melting time = 120 s Number of cycles = 40 Polymerase = KOD Template = 10 pmol Primer = 25 pmol Total volume = 25 ul ; _pdbx_entity_src_gen_prod_pcr.purification_details ; No purification ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_entity_src_gen_prod_pcr.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_pcr.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_prod_pcr.entry_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.entry_id' save_ save__pdbx_entity_src_gen_prod_pcr.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_pcr.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_prod_pcr.entity_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.entity_id' save_ save__pdbx_entity_src_gen_prod_pcr.step_id _item_description.description ; This item is the unique identifier for this PCR step. ; _item.name '_pdbx_entity_src_gen_prod_pcr.step_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_prod_pcr.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_prod_pcr.next_step_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_prod_pcr.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the PCR product. ; _item.name '_pdbx_entity_src_gen_prod_pcr.end_construct_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.end_construct_id' save_ save__pdbx_entity_src_gen_prod_pcr.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The referenced robot is the robot responsible for the PCR reaction (normally the heat cycler). ; _item.name '_pdbx_entity_src_gen_prod_pcr.robot_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.robot_id' save_ save__pdbx_entity_src_gen_prod_pcr.date _item_description.description ; The date of this production step. ; _item.name '_pdbx_entity_src_gen_prod_pcr.date' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_prod_pcr.forward_primer_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the forward primer. ; _item.name '_pdbx_entity_src_gen_prod_pcr.forward_primer_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code yes _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.forward_primer_id' save_ save__pdbx_entity_src_gen_prod_pcr.reverse_primer_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the reverse primer. ; _item.name '_pdbx_entity_src_gen_prod_pcr.reverse_primer_id' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code yes _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.reverse_primer_id' save_ save__pdbx_entity_src_gen_prod_pcr.reaction_details _item_description.description ; String value containing details of the PCR reaction. ; _item.name '_pdbx_entity_src_gen_prod_pcr.reaction_details' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_prod_pcr.purification_details _item_description.description ; String value containing details of any purification of the product of the PCR reaction. ; _item.name '_pdbx_entity_src_gen_prod_pcr.purification_details' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_prod_pcr.summary _item_description.description ; Summary of the details of the PCR reaction any purification of the product of the PCR reaction. ; _item.name '_pdbx_entity_src_gen_prod_pcr.summary' _item.category_id pdbx_entity_src_gen_prod_pcr _item.mandatory_code no _item_type.code text save_ ################################### # PDBX_ENTITY_SRC_GEN_PROD_DIGEST # ################################### # # _pdbx_entity_src_gen_prod_digest.entry_id # _pdbx_entity_src_gen_prod_digest.entity_id # _pdbx_entity_src_gen_prod_digest.step_id # _pdbx_entity_src_gen_prod_digest.next_step_id # _pdbx_entity_src_gen_prod_digest.restriction_enzyme_1 # _pdbx_entity_src_gen_prod_digest.restriction_enzyme_2 # _pdbx_entity_src_gen_prod_digest.purification_details # _pdbx_entity_src_gen_prod_digest.date # _pdbx_entity_src_gen_prod_digest.robot_id # # _pdbx_entity_src_gen_prod_digest.summary # save_pdbx_entity_src_gen_prod_digest _category.description ; This category contains details for the DIGEST steps used in the overall protein production process. The digestion is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step. ; _category.id pdbx_entity_src_gen_prod_digest _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_prod_digest.entry_id' '_pdbx_entity_src_gen_prod_digest.entity_id' '_pdbx_entity_src_gen_prod_digest.step_id' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example ; ; _pdbx_entity_src_gen_prod_digest.entry_id 111000111 _pdbx_entity_src_gen_prod_digest.entity_id 222000111 _pdbx_entity_src_gen_prod_digest.step_id 2 _pdbx_entity_src_gen_prod_digest.next_step_id 3 _pdbx_entity_src_gen_prod_digest.end_construct_id 440050000123 _pdbx_entity_src_gen_prod_digest.robot_id 5 _pdbx_entity_src_gen_prod_digest.date '2002-07-12:15:13' _pdbx_entity_src_gen_prod_digest.restriction_enzyme_1 'NcoI' _pdbx_entity_src_gen_prod_digest.restriction_enzyme_2 'BamII' _pdbx_entity_src_gen_prod_digest.purification_details ; No purification ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_entity_src_gen_prod_digest.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_digest.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_prod_digest.entry_id' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_digest.entry_id' save_ save__pdbx_entity_src_gen_prod_digest.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_prod_digest.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_prod_digest.entity_id' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_digest.entity_id' save_ save__pdbx_entity_src_gen_prod_digest.step_id _item_description.description ; This item is the unique identifier for this digestion step. ; _item.name '_pdbx_entity_src_gen_prod_digest.step_id' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_prod_digest.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_prod_digest.next_step_id' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_prod_digest.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the digest product ; _item.name '_pdbx_entity_src_gen_prod_digest.end_construct_id' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_digest.end_construct_id' save_ save__pdbx_entity_src_gen_prod_digest.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_prod_digest.robot_id' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code no _item_type.code code _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_prod_digest.robot_id' save_ save__pdbx_entity_src_gen_prod_digest.date _item_description.description ; The date of this production step. ; _item.name '_pdbx_entity_src_gen_prod_digest.date' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm _item_examples.case '2003-12-25' save_ save__pdbx_entity_src_gen_prod_digest.restriction_enzyme_1 _item_description.description ; The first enzyme used in the restriction digestion. The sites at which this cuts can be derived from the sequence. ; _item.name '_pdbx_entity_src_gen_prod_digest.restriction_enzyme_1' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code yes _item_type.code text _item_examples.case 'BamIII' save_ save__pdbx_entity_src_gen_prod_digest.restriction_enzyme_2 _item_description.description ; The second enzyme used in the restriction digestion. The sites at which this cuts can be derived from the sequence. ; _item.name '_pdbx_entity_src_gen_prod_digest.restriction_enzyme_2' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_prod_digest.purification_details _item_description.description ; String value containing details of any purification of the product of the digestion. ; _item.name '_pdbx_entity_src_gen_prod_digest.purification_details' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_prod_digest.summary _item_description.description ; Summary of the details of restriction digestion any purification of the product of the digestion. ; _item.name '_pdbx_entity_src_gen_prod_digest.summary' _item.category_id pdbx_entity_src_gen_prod_digest _item.mandatory_code no _item_type.code text save_ ######################## # ENTITY_SRC_GEN_CLONE # ######################## # # _pdbx_entity_src_gen_clone.entry_id # _pdbx_entity_src_gen_clone.entity_id # _pdbx_entity_src_gen_clone.step_id # _pdbx_entity_src_gen_clone.next_step_id # _pdbx_entity_src_gen_clone.end_construct_id # _pdbx_entity_src_gen_clone.robot_id # _pdbx_entity_src_gen_clone.date # _pdbx_entity_src_gen_clone.gene_insert_method # _pdbx_entity_src_gen_clone.vector_name # _pdbx_entity_src_gen_clone.vector_details # _pdbx_entity_src_gen_clone.transformation_method # _pdbx_entity_src_gen_clone.marker # _pdbx_entity_src_gen_clone.verification_method # _pdbx_entity_src_gen_clone.purification_details # # # _pdbx_entity_src_gen_clone.summary # save_pdbx_entity_src_gen_clone _category.description ; This category contains details for the cloning steps used in the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is provided data in the later two categories may be omitted. ; _category.id pdbx_entity_src_gen_clone _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_clone.entry_id' '_pdbx_entity_src_gen_clone.entity_id' '_pdbx_entity_src_gen_clone.step_id' save_ save__pdbx_entity_src_gen_clone.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_clone.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_clone.entry_id' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_clone.entry_id' save_ save__pdbx_entity_src_gen_clone.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_clone.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_clone.entity_id' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_clone.entity_id' save_ save__pdbx_entity_src_gen_clone.step_id _item_description.description ; This item is the unique identifier for this cloning step. ; _item.name '_pdbx_entity_src_gen_clone.step_id' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_clone.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_clone.next_step_id' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_clone.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the cloned product. ; _item.name '_pdbx_entity_src_gen_clone.end_construct_id' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_clone.end_construct_id' save_ save__pdbx_entity_src_gen_clone.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_clone.robot_id' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_clone.robot_id' save_ save__pdbx_entity_src_gen_clone.date _item_description.description ; The date of this production step. ; _item.name '_pdbx_entity_src_gen_clone.date' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_clone.gene_insert_method _item_description.description ; The method used to insert the gene into the vector. For 'Ligation', an PDBX_ENTITY_SRC_GEN_CLONE_LIGATION entry with matching .step_id is expected. For 'Recombination', an PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION entry with matching .step_id is expected. ; _item.name '_pdbx_entity_src_gen_clone.gene_insert_method' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail L 'Ligation' R 'Recombination' save_ save__pdbx_entity_src_gen_clone.vector_name _item_description.description ; The name of the vector used in this cloning step. ; _item.name '_pdbx_entity_src_gen_clone.vector_name' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_clone.vector_details _item_description.description ; Details of any modifications made to the named vector. ; _item.name '_pdbx_entity_src_gen_clone.vector_details' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_clone.transformation_method _item_description.description ; The method used to transform the expression cell line with the vector ; _item.name '_pdbx_entity_src_gen_clone.transformation_method' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail H 'Heat shock' E 'Electroporation' C 'Calcium shock' save_ save__pdbx_entity_src_gen_clone.marker _item_description.description ; The type of marker included to allow selection of transformed cells ; _item.name '_pdbx_entity_src_gen_clone.marker' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail A 'Antibiotic resistance' F 'Fluorescence' save_ save__pdbx_entity_src_gen_clone.verification_method _item_description.description ; The method used to verify that the incorporated gene is correct ; _item.name '_pdbx_entity_src_gen_clone.verification_method' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail P 'PCR on plasmid' R 'Restriction enzyme digestion' D 'DNA sequencing' save_ save__pdbx_entity_src_gen_clone.purification_details _item_description.description ; Details of any purification of the product. ; _item.name '_pdbx_entity_src_gen_clone.purification_details' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_clone.summary _item_description.description ; Summary of ligation or recombionation cloning used, the associated verification method and any purification of the product. ; _item.name '_pdbx_entity_src_gen_clone.summary' _item.category_id pdbx_entity_src_gen_clone _item.mandatory_code no _item_type.code text save_ ###################################### # PDBX_ENTITY_SRC_GEN_CLONE_LIGATION # ###################################### # # _pdbx_entity_src_gen_clone_ligation.entry_id # _pdbx_entity_src_gen_clone_ligation.entity_id # _pdbx_entity_src_gen_clone_ligation.step_id # _pdbx_entity_src_gen_clone_ligation.cleavage_enzymes # _pdbx_entity_src_gen_clone_ligation.ligation_enzymes # _pdbx_entity_src_gen_clone_ligation.temperature # _pdbx_entity_src_gen_clone_ligation.time # _pdbx_entity_src_gen_clone_ligation.details # save_pdbx_entity_src_gen_clone_ligation _category.description ; This category contains details for the ligation-based cloning steps used in the overall protein production process. _pdbx_entity_src_gen_clone_ligation.clone_step_id in this category must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in PDBX_ENTITY_SRC_GEN_CLONE_LIGATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover ligation dependent cloning steps. ; _category.id pdbx_entity_src_gen_clone_ligation _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_clone_ligation.entry_id' '_pdbx_entity_src_gen_clone_ligation.entity_id' '_pdbx_entity_src_gen_clone_ligation.step_id' save_ save__pdbx_entity_src_gen_clone_ligation.entry_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_clone.entry_id in the PDBX_ENTITY_SRC_GEN_CLONE category. ; _item.name '_pdbx_entity_src_gen_clone_ligation.entry_id' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_clone.entry_id' _item_linked.child_name '_pdbx_entity_src_gen_clone_ligation.entry_id' save_ save__pdbx_entity_src_gen_clone_ligation.entity_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_clone.entity_id in the PDBX_ENTITY_SRC_GEN_CLONE category. ; _item.name '_pdbx_entity_src_gen_clone_ligation.entity_id' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_clone.entity_id' _item_linked.child_name '_pdbx_entity_src_gen_clone_ligation.entity_id' save_ save__pdbx_entity_src_gen_clone_ligation.step_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_clone.step_id in the PDBX_ENTITY_SRC_GEN_CLONE category. ; _item.name '_pdbx_entity_src_gen_clone_ligation.step_id' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_clone.step_id' _item_linked.child_name '_pdbx_entity_src_gen_clone_ligation.step_id' save_ save__pdbx_entity_src_gen_clone_ligation.cleavage_enzymes _item_description.description ; The names of the enzymes used to cleave the vector. In addition an enzyme used to blunt the cut ends, etc., should be named here. ; _item.name '_pdbx_entity_src_gen_clone_ligation.cleavage_enzymes' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_clone_ligation.ligation_enzymes _item_description.description ; The names of the enzymes used to ligate the gene into the cleaved vector. ; _item.name '_pdbx_entity_src_gen_clone_ligation.ligation_enzymes' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_clone_ligation.temperature _item_description.description ; The temperature at which the ligation experiment was performed, in degrees celsius. ; _item.name '_pdbx_entity_src_gen_clone_ligation.temperature' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code yes _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_clone_ligation.time _item_description.description ; The duration of the ligation reaction in minutes. ; _item.name '_pdbx_entity_src_gen_clone_ligation.time' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code yes _item_type.code int _item_units.code minutes save_ save__pdbx_entity_src_gen_clone_ligation.details _item_description.description ; Any details to be associated with this ligation step, e.g. the protocol. ; _item.name '_pdbx_entity_src_gen_clone_ligation.details' _item.category_id pdbx_entity_src_gen_clone_ligation _item.mandatory_code no _item_type.code text save_ ########################################### # PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION # ########################################### # # _pdbx_entity_src_gen_clone_recombination.entry__id # _pdbx_entity_src_gen_clone_recombination.entity_id # _pdbx_entity_src_gen_clone_recombination.step_id # _pdbx_entity_src_gen_clone_recombination.system # _pdbx_entity_src_gen_clone_recombination.recombination_enzymes # _pdbx_entity_src_gen_clone_recombination.details # save_pdbx_entity_src_gen_clone_recombination _category.description ; This category contains details for the recombination-based cloning steps used in the overall protein production process. It is assumed that these reactions will use commercially available kits. _pdbx_entity_src_gen_clone_recombination.clone_step_id in this category must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover recombination dependent cloning steps. ; _category.id pdbx_entity_src_gen_clone_recombination _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_clone_recombination.entry_id' '_pdbx_entity_src_gen_clone_recombination.entity_id' '_pdbx_entity_src_gen_clone_recombination.step_id' save_ save__pdbx_entity_src_gen_clone_recombination.entry_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_clone.entry_id in the PDBX_ENTITY_SRC_GEN_CLONE category. ; _item.name '_pdbx_entity_src_gen_clone_recombination.entry_id' _item.category_id pdbx_entity_src_gen_clone_recombination _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_clone.entry_id' _item_linked.child_name '_pdbx_entity_src_gen_clone_recombination.entry_id' save_ save__pdbx_entity_src_gen_clone_recombination.entity_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_clone.entity_id in the PDBX_ENTITY_SRC_GEN_CLONE category. ; _item.name '_pdbx_entity_src_gen_clone_recombination.entity_id' _item.category_id pdbx_entity_src_gen_clone_recombination _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_clone.entity_id' _item_linked.child_name '_pdbx_entity_src_gen_clone_recombination.entity_id' save_ save__pdbx_entity_src_gen_clone_recombination.step_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_clone.step_id in the PDBX_ENTITY_SRC_GEN_CLONE category. ; _item.name '_pdbx_entity_src_gen_clone_recombination.step_id' _item.category_id pdbx_entity_src_gen_clone_recombination _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_clone.step_id' _item_linked.child_name '_pdbx_entity_src_gen_clone_recombination.step_id' save_ save__pdbx_entity_src_gen_clone_recombination.system _item_description.description ; The name of the recombination system. ; _item.name '_pdbx_entity_src_gen_clone_recombination.system' _item.category_id pdbx_entity_src_gen_clone_recombination _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail G 'Gateway Tm' I 'Infusion/Creator Tm' N 'Novagen's system - name?' save_ save__pdbx_entity_src_gen_clone_recombination.recombination_enzymes _item_description.description ; The names of the enzymes used for this recombination step. ; _item.name '_pdbx_entity_src_gen_clone_recombination.recombination_enzymes' _item.category_id pdbx_entity_src_gen_clone_recombination _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail B 'Gateway BP clonase' L 'Gateway LR clonase' T 'Topoisomerase' C 'Cre recombinase' I 'Infusion enzyme - name?' save_ save__pdbx_entity_src_gen_clone_recombination.details _item_description.description ; Any details to be associated with this recombination step, e.g. the protocol or differences from the manufacturer's specified protocol. ; _item.name '_pdbx_entity_src_gen_clone_recombination.details' _item.category_id pdbx_entity_src_gen_clone_recombination _item.mandatory_code no _item_type.code text save_ ############################### # PDBX_ENTITY_SRC_GEN_EXPRESS # ############################### # # _pdbx_entity_src_gen_express.entry_id # _pdbx_entity_src_gen_express.entity_id # _pdbx_entity_src_gen_express.step_id # _pdbx_entity_src_gen_express.next_step_id # _pdbx_entity_src_gen_express.end_construct_id # _pdbx_entity_src_gen_express.robot_id # _pdbx_entity_src_gen_express.date # _pdbx_entity_src_gen_express.promoter_type # _pdbx_entity_src_gen_express.plasmid_id # _pdbx_entity_src_gen_express.vector_type # _pdbx_entity_src_gen_express.N_terminal_seq_tag # _pdbx_entity_src_gen_express.C_terminal_seq_tag # _pdbx_entity_src_gen_express.host_org_scientific_name # _pdbx_entity_src_gen_express.host_org_common_name # _pdbx_entity_src_gen_express.host_org_variant # _pdbx_entity_src_gen_express.host_org_strain # _pdbx_entity_src_gen_express.host_org_tissue # _pdbx_entity_src_gen_express.host_org_tax_id # _pdbx_entity_src_gen_express.host_org_culture_collection # _pdbx_entity_src_gen_express.host_org_cell_line # _pdbx_entity_src_gen_express.host_org_details # _pdbx_entity_src_gen_express.culture_base_media # _pdbx_entity_src_gen_express.culture_additives # _pdbx_entity_src_gen_express.culture_volume # _pdbx_entity_src_gen_express.culture_time # _pdbx_entity_src_gen_express.culture_temperature # _pdbx_entity_src_gen_express.inducer # _pdbx_entity_src_gen_express.inducer_concentration # _pdbx_entity_src_gen_express.induction_details # _pdbx_entity_src_gen_express.multiplicity_of_infection # _pdbx_entity_src_gen_express.induction_growth_time # _pdbx_entity_src_gen_express.induction_temperature # _pdbx_entity_src_gen_express.harvesting_details # _pdbx_entity_src_gen_express.storage_details # # _pdbx_entity_src_gen_express.summary # save_pdbx_entity_src_gen_express _category.description ; This category contains details for the EXPRESSION steps used in the overall protein production process. It is hoped that this category will cover all forms of cell-based expression by reading induction as induction/transformation/transfection. ; _category.id pdbx_entity_src_gen_express _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_express.entry_id' '_pdbx_entity_src_gen_express.entity_id' '_pdbx_entity_src_gen_express.step_id' save_ save__pdbx_entity_src_gen_express.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_express.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_express.entry_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code code _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_express.entry_id' save_ save__pdbx_entity_src_gen_express.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_express.entity_id uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_express.entity_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code code _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_express.entity_id' save_ save__pdbx_entity_src_gen_express.step_id _item_description.description ; This item is the unique identifier for this expression step. ; _item.name '_pdbx_entity_src_gen_express.step_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_express.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_express.next_step_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_express.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product. ; _item.name '_pdbx_entity_src_gen_express.end_construct_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code int _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_express.end_construct_id' save_ save__pdbx_entity_src_gen_express.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_express.robot_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_express.robot_id' save_ save__pdbx_entity_src_gen_express.date _item_description.description ; The date of production step. ; _item.name '_pdbx_entity_src_gen_express.date' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_express.promoter_type _item_description.description ; The nature of the promoter controlling expression of the gene. ; _item.name '_pdbx_entity_src_gen_express.promoter_type' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code text _item_examples.case 'T7 LacZ' save_ save__pdbx_entity_src_gen_express.plasmid_id _item_description.description ; This item is a pointer to _pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced entry will contain the nucleotide sequence that is to be expressed, including tags. ; _item.name '_pdbx_entity_src_gen_express.plasmid_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code code _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_express.plasmid_id' save_ save__pdbx_entity_src_gen_express.vector_type _item_description.description ; Identifies the type of vector used (plasmid, virus, or cosmid) in the expression system. ; _item.name '_pdbx_entity_src_gen_express.vector_type' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code code save_ save__pdbx_entity_src_gen_express.N_terminal_seq_tag _item_description.description ; Any N-terminal sequence tag as a string of one letter amino acid codes. ; _item.name '_pdbx_entity_src_gen_express.N_terminal_seq_tag' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_express.C_terminal_seq_tag _item_description.description ; Any C-terminal sequence tag as a string of one letter amino acid codes ; _item.name '_pdbx_entity_src_gen_express.C_terminal_seq_tag' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_express.host_org_scientific_name _item_description.description ; The scientific name of the organism that served as host for the expression system. It is expected that either this item or _pdbx_entity_src_gen_express.host_org_tax_id should be populated. ; _item.name '_pdbx_entity_src_gen_express.host_org_scientific_name' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_common_name _item_description.description ; The common name of the organism that served as host for the expression system. Where _pdbx_entity_src_gen_express.host_org_tax_id is populated it is expected that this item may be derived by look up against the taxonomy database. ; _item.name '_pdbx_entity_src_gen_express.host_org_common_name' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_variant _item_description.description ; The vairant of the organism that served as host for the expression system. Where _pdbx_entity_src_gen_express.host_org_tax_id is populated it is expected that this item may be derived by a look up against the taxonomy database. ; _item.name '_pdbx_entity_src_gen_express.host_org_variant' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_strain _item_description.description ; The strain of the organism that served as host for the expression system. Where _pdbx_entity_src_gen_express.host_org_tax_id is populated it is expected that this item may be derived by a look up against the taxonomy database. ; _item.name '_pdbx_entity_src_gen_express.host_org_strain' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_tissue _item_description.description ; The specific tissue which expressed the molecule. ; _item.name '_pdbx_entity_src_gen_express.host_org_tissue' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_culture_collection _item_description.description ; Culture collection of the expression system ; _item.name '_pdbx_entity_src_gen_express.host_org_culture_collection' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_cell_line _item_description.description ; A specific line of cells used as the expression system ; _item.name '_pdbx_entity_src_gen_express.host_org_cell_line' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_tax_id _item_description.description ; The id for the NCBI taxonomy node corresponding to the organism that served as host for the expression system. ; _item.name '_pdbx_entity_src_gen_express.host_org_tax_id' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.host_org_details _item_description.description ; A description of special aspects of the organism that served as host for the expression system. ; _item.name '_pdbx_entity_src_gen_express.host_org_details' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_express.culture_base_media _item_description.description ; The name of the base media in which the expression host was grown. ; _item.name '_pdbx_entity_src_gen_express.culture_base_media' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_express.culture_additives _item_description.description ; Any additives to the base media in which the expression host was grown. ; _item.name '_pdbx_entity_src_gen_express.culture_additives' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_express.culture_volume _item_description.description ; The volume of media in milliliters in which the expression host was grown. ; _item.name '_pdbx_entity_src_gen_express.culture_volume' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code float _item_units.code milliliters save_ save__pdbx_entity_src_gen_express.culture_time _item_description.description ; The time in hours for which the expression host was allowed to grow prior to induction/transformation/transfection. ; _item.name '_pdbx_entity_src_gen_express.culture_time' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code float _item_units.code hours save_ save__pdbx_entity_src_gen_express.culture_temperature _item_description.description ; The temperature in degrees celsius at which the expression host was allowed to grow prior to induction/transformation/transfection. ; _item.name '_pdbx_entity_src_gen_express.culture_temperature' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_express.inducer _item_description.description ; The chemical name of the inducing agent. ; _item.name '_pdbx_entity_src_gen_express.inducer' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code line save_ save__pdbx_entity_src_gen_express.inducer_concentration _item_description.description ; Concentration of the inducing agent. ; _item.name '_pdbx_entity_src_gen_express.inducer_concentration' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code float _item_units.code mg_per_ml save_ save__pdbx_entity_src_gen_express.induction_details _item_description.description ; Details of induction/transformation/transfection. ; _item.name '_pdbx_entity_src_gen_express.induction_details' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_express.multiplicity_of_infection _item_description.description ; The multiplicity of infection for genes introduced by transfection, eg. for baculovirus-based expression. ; _item.name '_pdbx_entity_src_gen_express.multiplicity_of_infection' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code float _item_units.code arbitrary save_ save__pdbx_entity_src_gen_express.induction_timepoint _item_description.description ; The time in hours after induction/transformation/transfection at which the optical density of the culture was measured. ; _item.name '_pdbx_entity_src_gen_express.induction_timepoint' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code float _item_units.code hours save_ save__pdbx_entity_src_gen_express.induction_temperature _item_description.description ; The temperature in celsius at which the induced/transformed/transfected cells were grown. ; _item.name '_pdbx_entity_src_gen_express.induction_temperature' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code yes _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_express.harvesting_details _item_description.description ; Details of the harvesting protocol. ; _item.name '_pdbx_entity_src_gen_express.harvesting_details' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_express.storage_details _item_description.description ; Details of how the harvested culture was stored. ; _item.name '_pdbx_entity_src_gen_express.storage_details' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_express.summary _item_description.description ; Summary of the details of the expression steps used in protein production. ; _item.name '_pdbx_entity_src_gen_express.summary' _item.category_id pdbx_entity_src_gen_express _item.mandatory_code no _item_type.code text save_ ######################################### # PDBX_ENTITY_SRC_GEN_EXPRESS_TIMEPOINT # ######################################### # # _pdbx_entity_src_gen_express_timepoint.entry_id # _pdbx_entity_src_gen_express_timepoint.entity_id # _pdbx_entity_src_gen_express_timepoint.step_id # _pdbx_entity_src_gen_express_timepoint.serial # _pdbx_entity_src_gen_express_timepoint.time # _pdbx_entity_src_gen_express_timepoint.OD # save_pdbx_entity_src_gen_express_timepoint _category.description ; This category contains details for OD time series used to monitor a given EXPRESSION step used in the overall protein production process. ; _category.id pdbx_entity_src_gen_express_timepoint _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_express_timepoint.entry_id' '_pdbx_entity_src_gen_express_timepoint.entity_id' '_pdbx_entity_src_gen_express_timepoint.step_id' '_pdbx_entity_src_gen_express_timepoint.serial' save_ save__pdbx_entity_src_gen_express_timepoint.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_express_timepoint.entry_id is a pointer to _pdbx_entity_src_gen_express.entry_id ; _item.name '_pdbx_entity_src_gen_express_timepoint.entry_id' _item.category_id pdbx_entity_src_gen_express_timepoint _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_express.entry_id' _item_linked.child_name '_pdbx_entity_src_gen_express_timepoint.entry_id' save_ save__pdbx_entity_src_gen_express_timepoint.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_express_timepoint.entity_id is a pointer to _pdbx_entity_src_gen_express.entity_id ; _item.name '_pdbx_entity_src_gen_express_timepoint.entity_id' _item.category_id pdbx_entity_src_gen_express_timepoint _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_express.entity_id' _item_linked.child_name '_pdbx_entity_src_gen_express_timepoint.entity_id' save_ save__pdbx_entity_src_gen_express_timepoint.step_id _item_description.description ; This item is a pointer to _pdbx_entity_src_gen_express.step_id ; _item.name '_pdbx_entity_src_gen_express_timepoint.step_id' _item.category_id pdbx_entity_src_gen_express_timepoint _item.mandatory_code yes _item_linked.parent_name '_pdbx_entity_src_gen_express.step_id' _item_linked.child_name '_pdbx_entity_src_gen_express_timepoint.step_id' save_ save__pdbx_entity_src_gen_express_timepoint.serial _item_description.description ; This items uniquely defines a timepoint within a series. ; _item.name '_pdbx_entity_src_gen_express_timepoint.serial' _item.category_id pdbx_entity_src_gen_express_timepoint _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_express_timepoint.OD _item_description.description ; The optical density of the expression culture in arbitrary units at the timepoint specified. ; _item.name '_pdbx_entity_src_gen_express_timepoint.OD' _item.category_id pdbx_entity_src_gen_express_timepoint _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_express_timepoint.time _item_description.description ; The time in hours after induction/transformation/transfection at which the optical density of the culture was measured. ; _item.name '_pdbx_entity_src_gen_express_timepoint.time' _item.category_id pdbx_entity_src_gen_express_timepoint _item.mandatory_code yes _item_type.code int save_ ############################# # PDBX_ENTITY_SRC_GEN_LYSIS # ############################# # # _pdbx_entity_src_gen_lysis.entry_id # _pdbx_entity_src_gen_lysis.entity_id # _pdbx_entity_src_gen_lysis.step_id # _pdbx_entity_src_gen_lysis.next_step_id # _pdbx_entity_src_gen_lysis.end_construct_id # _pdbx_entity_src_gen_lysis.date # _pdbx_entity_src_gen_lysis.robot_id # _pdbx_entity_src_gen_lysis.method # _pdbx_entity_src_gen_lysis.buffer_id # _pdbx_entity_src_gen_lysis.buffer_volume # _pdbx_entity_src_gen_lysis.temperature # _pdbx_entity_src_gen_lysis.time # _pdbx_entity_src_gen_lysis.details # save_pdbx_entity_src_gen_lysis _category.description ; This category contains details for the cell lysis steps used in the overall protein production process. ; _category.id pdbx_entity_src_gen_lysis _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_lysis.entry_id' '_pdbx_entity_src_gen_lysis.entity_id' '_pdbx_entity_src_gen_lysis.step_id' save_ save__pdbx_entity_src_gen_lysis.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_lysis.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_lysis.entry_id' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_lysis.entry_id' save_ save__pdbx_entity_src_gen_lysis.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_lysis.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_lysis.entity_id' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_lysis.entity_id' save_ save__pdbx_entity_src_gen_lysis.step_id _item_description.description ; This item is the unique identifier for this lysis step. ; _item.name '_pdbx_entity_src_gen_lysis.step_id' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_lysis.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_lysis.next_step_id' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_lysis.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after lysis. ; _item.name '_pdbx_entity_src_gen_lysis.end_construct_id' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_lysis.end_construct_id' save_ save__pdbx_entity_src_gen_lysis.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_lysis.robot_id' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_lysis.robot_id' save_ save__pdbx_entity_src_gen_lysis.date _item_description.description ; The date of this production step. ; _item.name '_pdbx_entity_src_gen_lysis.date' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_lysis.method _item_description.description ; The lysis method. ; _item.name '_pdbx_entity_src_gen_lysis.method' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail S 'Sonication' D 'Detergent' B 'Sonication and detergent' save_ save__pdbx_entity_src_gen_lysis.buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the lysis was performed. ; _item.name '_pdbx_entity_src_gen_lysis.buffer_id' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_type.code code _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_lysis.buffer_id' save_ save__pdbx_entity_src_gen_lysis.buffer_volume _item_description.description ; The volume in milliliters of buffer in which the lysis was performed. ; _item.name '_pdbx_entity_src_gen_lysis.buffer_volume' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_type.code float _item_units.code milliliters save_ save__pdbx_entity_src_gen_lysis.temperature _item_description.description ; The temperature in degrees celsius at which the lysis was performed. ; _item.name '_pdbx_entity_src_gen_lysis.temperature' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_lysis.time _item_description.description ; The time in seconds of the lysis experiment. ; _item.name '_pdbx_entity_src_gen_lysis.time' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code yes _item_type.code float _item_units.code minutes save_ save__pdbx_entity_src_gen_lysis.details _item_description.description ; String value containing details of the lysis protocol. ; _item.name '_pdbx_entity_src_gen_lysis.details' _item.category_id pdbx_entity_src_gen_lysis _item.mandatory_code no _item_type.code text save_ ############################## # PDBX_ENTITY_SRC_GEN_REFOLD # ############################## # # _pdbx_entity_src_gen_refold.entry_id # _pdbx_entity_src_gen_refold.entity_id # _pdbx_entity_src_gen_refold.step_id # _pdbx_entity_src_gen_refold.next_step_id # _pdbx_entity_src_gen_refold.end_construct_id # _pdbx_entity_src_gen_refold.robot_id # _pdbx_entity_src_gen_refold.date # _pdbx_entity_src_gen_refold.denature_buffer_id # _pdbx_entity_src_gen_refold.refold_buffer_id # _pdbx_entity_src_gen_refold.temperature # _pdbx_entity_src_gen_refold.time # _pdbx_entity_src_gen_refold.storage_buffer_id # _pdbx_entity_src_gen_refold.details # save_pdbx_entity_src_gen_refold _category.description ; This category contains details for the refolding steps used in the overall protein production process. ; _category.id pdbx_entity_src_gen_refold _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_refold.entry_id' '_pdbx_entity_src_gen_refold.entity_id' '_pdbx_entity_src_gen_refold.step_id' save_ save__pdbx_entity_src_gen_refold.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_refold.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_refold.entry_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_refold.entry_id' save_ save__pdbx_entity_src_gen_refold.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_refold.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_refold.entity_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_refold.entity_id' save_ save__pdbx_entity_src_gen_refold.step_id _item_description.description ; This item is the unique identifier for this refolding step. ; _item.name '_pdbx_entity_src_gen_refold.step_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_refold.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_refold.next_step_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_refold.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the refolding step. ; _item.name '_pdbx_entity_src_gen_refold.end_construct_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_refold.end_construct_id' save_ save__pdbx_entity_src_gen_refold.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_refold.robot_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_refold.robot_id' save_ save__pdbx_entity_src_gen_refold.date _item_description.description ; The date of this production step. ; _item.name '_pdbx_entity_src_gen_refold.date' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_refold.denature_buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was denatured. ; _item.name '_pdbx_entity_src_gen_refold.denature_buffer_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_refold.denature_buffer_id' save_ save__pdbx_entity_src_gen_refold.refold_buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was refolded. ; _item.name '_pdbx_entity_src_gen_refold.refold_buffer_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_refold.refold_buffer_id' save_ save__pdbx_entity_src_gen_refold.temperature _item_description.description ; The temperature in degrees celsius at which the protein was refolded. ; _item.name '_pdbx_entity_src_gen_refold.temperature' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_refold.time _item_description.description ; The time in hours over which the protein was refolded. ; _item.name '_pdbx_entity_src_gen_refold.time' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_type.code float _item_units.code hours save_ save__pdbx_entity_src_gen_refold.storage_buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the refolded protein was stored. ; _item.name '_pdbx_entity_src_gen_refold.storage_buffer_id' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code yes _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_refold.storage_buffer_id' save_ save__pdbx_entity_src_gen_refold.details _item_description.description ; String value containing details of the refolding. ; _item.name '_pdbx_entity_src_gen_refold.details' _item.category_id pdbx_entity_src_gen_refold _item.mandatory_code no _item_type.code text save_ ################################### # PDBX_ENTITY_SRC_GEN_PROTEOLYSIS # ################################### # # _pdbx_entity_src_gen_proteolysis.entry_id # _pdbx_entity_src_gen_proteolysis.entity_id # _pdbx_entity_src_gen_proteolysis.step_id # _pdbx_entity_src_gen_proteolysis.next_step_id # _pdbx_entity_src_gen_proteolysis.end_construct_id # _pdbx_entity_src_gen_proteolysis.date # _pdbx_entity_src_gen_proteolysis.robot_id # _pdbx_entity_src_gen_proteolysis.details # _pdbx_entity_src_gen_proteolysis.protease # _pdbx_entity_src_gen_proteolysis.protein_protease_ratio # _pdbx_entity_src_gen_proteolysis.cleavage_buffer # _pdbx_entity_src_gen_proteolysis.cleavage_temperature # _pdbx_entity_src_gen_proteolysis.cleavage_time # save_pdbx_entity_src_gen_proteolysis _category.description ; This category contains details for the protein purification tag removal steps used in the overall protein production process ; _category.id pdbx_entity_src_gen_proteolysis _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_proteolysis.entry_id' '_pdbx_entity_src_gen_proteolysis.entity_id' '_pdbx_entity_src_gen_proteolysis.step_id' save_ save__pdbx_entity_src_gen_proteolysis.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_proteolysis.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_proteolysis.entry_id' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_proteolysis.entry_id' save_ save__pdbx_entity_src_gen_proteolysis.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_proteolysis.entity_id uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_proteolysis.entity_id' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_proteolysis.entity_id' save_ save__pdbx_entity_src_gen_proteolysis.step_id _item_description.description ; This item is the unique identifier for this tag removal step. ; _item.name '_pdbx_entity_src_gen_proteolysis.step_id' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_proteolysis.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_proteolysis.next_step_id' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_proteolysis.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the proteolysis step. ; _item.name '_pdbx_entity_src_gen_proteolysis.end_construct_id' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_proteolysis.end_construct_id' save_ save__pdbx_entity_src_gen_proteolysis.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_proteolysis.robot_id' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_proteolysis.robot_id' save_ save__pdbx_entity_src_gen_proteolysis.date _item_description.description ; The date of production step. ; _item.name '_pdbx_entity_src_gen_proteolysis.date' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_proteolysis.details _item_description.description ; Details of this tag removal step. ; _item.name '_pdbx_entity_src_gen_proteolysis.details' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_proteolysis.protease _item_description.description ; The name of the protease used for cleavage. ; _item.name '_pdbx_entity_src_gen_proteolysis.protease' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_proteolysis.protein_protease_ratio _item_description.description ; The ratio of protein to protease used for the cleavage. = mol protein / mol protease ; _item.name '_pdbx_entity_src_gen_proteolysis.protein_protease_ratio' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_type.code float save_ save__pdbx_entity_src_gen_proteolysis.cleavage_buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the cleavage was performed. ; _item.name '_pdbx_entity_src_gen_proteolysis.cleavage_buffer_id' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_proteolysis.cleavage_buffer_id' save_ save__pdbx_entity_src_gen_proteolysis.cleavage_temperature _item_description.description ; The temperature in degrees celsius at which the cleavage was performed. ; _item.name '_pdbx_entity_src_gen_proteolysis.cleavage_temperature' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_proteolysis.cleavage_time _item_description.description ; The time in minutes for the cleavage reaction ; _item.name '_pdbx_entity_src_gen_proteolysis.cleavage_time' _item.category_id pdbx_entity_src_gen_proteolysis _item.mandatory_code no _item_type.code float _item_units.code minutes save_ ############################# # PDBX_ENTITY_SRC_GEN_CHROM # ############################# # # _pdbx_entity_src_gen_chrom.entry_id # _pdbx_entity_src_gen_chrom.entity_id # _pdbx_entity_src_gen_chrom.step_id # _pdbx_entity_src_gen_chrom.next_step_id # _pdbx_entity_src_gen_chrom.end_construct_id # _pdbx_entity_src_gen_chrom.robot_id # _pdbx_entity_src_gen_chrom.date # _pdbx_entity_src_gen_chrom.column_type # _pdbx_entity_src_gen_chrom.column_volume # _pdbx_entity_src_gen_chrom.column_temperature # _pdbx_entity_src_gen_chrom.equilibration_buffer # _pdbx_entity_src_gen_chrom.flow_rate # _pdbx_entity_src_gen_chrom.elution_protocol # _pdbx_entity_src_gen_chrom.sample_prep_details # _pdbx_entity_src_gen_chrom.sample_volume # _pdbx_entity_src_gen_chrom.protein_concentration # _pdbx_entity_src_gen_chrom.volume_fraction # _pdbx_entity_src_gen_chrom.volume_pooled_fractions # _pdbx_entity_src_gen_chrom.yield_pooled_fractions # _pdbx_entity_src_gen_chrom.yield_method # _pdbx_entity_src_gen_chrom.post_treatment save_pdbx_entity_src_gen_chrom _category.description ; This category contains details for the chromatographic steps used in the purification of the protein. ; _category.id pdbx_entity_src_gen_chrom _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_chrom.entry_id' '_pdbx_entity_src_gen_chrom.entity_id' '_pdbx_entity_src_gen_chrom.step_id' save_ save__pdbx_entity_src_gen_chrom.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_chrom.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_chrom.entry_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_chrom.entry_id' save_ save__pdbx_entity_src_gen_chrom.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_chrom.entity_id uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_chrom.entity_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_chrom.entity_id' save_ save__pdbx_entity_src_gen_chrom.step_id _item_description.description ; This item is the unique identifier for this chromatography step. ; _item.name '_pdbx_entity_src_gen_chrom.step_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_chrom.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_chrom.next_step_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_chrom.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the chromatography step. ; _item.name '_pdbx_entity_src_gen_chrom.end_construct_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_chrom.end_construct_id' save_ save__pdbx_entity_src_gen_chrom.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_chrom.robot_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_chrom.robot_id' save_ save__pdbx_entity_src_gen_chrom.date _item_description.description ; The date of production step. ; _item.name '_pdbx_entity_src_gen_chrom.date' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_chrom.column_type _item_description.description ; The type of column used in this step. ; _item.name '_pdbx_entity_src_gen_chrom.column_type' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_chrom.column_volume _item_description.description ; The volume of the column used in this step. ; _item.name '_pdbx_entity_src_gen_chrom.column_volume' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code float _item_units.code milliliters save_ save__pdbx_entity_src_gen_chrom.column_temperature _item_description.description ; The temperature in degrees celsius at which this column was run. ; _item.name '_pdbx_entity_src_gen_chrom.column_temperature' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_chrom.equilibration_buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the column was equilibrated. ; _item.name '_pdbx_entity_src_gen_chrom.equilibration_buffer_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_chrom.equilibration_buffer_id' save_ save__pdbx_entity_src_gen_chrom.flow_rate _item_description.description ; The rate at which the equilibration buffer flowed through the column. ; _item.name '_pdbx_entity_src_gen_chrom.flow_rate' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_type.code float _item_units.code ml_per_min save_ save__pdbx_entity_src_gen_chrom.elution_buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that with which the protein was eluted. ; _item.name '_pdbx_entity_src_gen_chrom.elution_buffer_id' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_chrom.elution_buffer_id' save_ save__pdbx_entity_src_gen_chrom.elution_protocol _item_description.description ; Details of the elution protocol. ; _item.name '_pdbx_entity_src_gen_chrom.elution_protocol' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_chrom.sample_prep_details _item_description.description ; Details of the sample preparation prior to running the column. ; _item.name '_pdbx_entity_src_gen_chrom.sample_prep_details' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_chrom.sample_volume _item_description.description ; The volume of protein solution run on the column. ; _item.name '_pdbx_entity_src_gen_chrom.sample_volume' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code float _item_units.code milliliters save_ save__pdbx_entity_src_gen_chrom.sample_concentration _item_description.description ; The concentration of the protein solution put onto the column. ; _item.name '_pdbx_entity_src_gen_chrom.sample_concentration' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_type.code float _item_units.code mg_per_ml save_ save__pdbx_entity_src_gen_chrom.sample_conc_method _item_description.description ; The method used to determine the concentration of the protein solution put onto the column. ; _item.name '_pdbx_entity_src_gen_chrom.sample_conc_method' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_chrom.volume_pooled_fractions _item_description.description ; The total volume of all the fractions pooled to give the purified protein solution. ; _item.name '_pdbx_entity_src_gen_chrom.volume_pooled_fractions' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code float _item_units.code milliliters save_ save__pdbx_entity_src_gen_chrom.yield_pooled_fractions _item_description.description ; The yield in milligrams of protein recovered in the pooled fractions. ; _item.name '_pdbx_entity_src_gen_chrom.yield_pooled_fractions' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code float _item_units.code milligrams save_ save__pdbx_entity_src_gen_chrom.yield_method _item_description.description ; The method used to determine the yield ; _item.name '_pdbx_entity_src_gen_chrom.yield_method' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_chrom.post_treatment _item_description.description ; Details of any post-chromatographic treatment of the protein sample. ; _item.name '_pdbx_entity_src_gen_chrom.post_treatment' _item.category_id pdbx_entity_src_gen_chrom _item.mandatory_code no _item_type.code text save_ ############################# # PDBX_ENTITY_SRC_GEN_FRACT # ############################# # # _pdbx_entity_src_gen_fract.entry_id # _pdbx_entity_src_gen_fract.entity_id # _pdbx_entity_src_gen_fract.step_id # _pdbx_entity_src_gen_fract.next_step_id # _pdbx_entity_src_gen_fract.end_construct_id # _pdbx_entity_src_gen_fract.robot_id # _pdbx_entity_src_gen_fract.date # _pdbx_entity_src_gen_fract.method # _pdbx_entity_src_gen_fract.temperature # _pdbx_entity_src_gen_fract.details # _pdbx_entity_src_gen_fract.protein_location # _pdbx_entity_src_gen_fract.protein_yield # _pdbx_entity_src_gen_fract.protein_yield_method # save_pdbx_entity_src_gen_fract _category.description ; This category contains details for the fraction steps used in the overall protein production process. Examples of fractionation steps are centrifugation and magnetic bead pull-down purification. ; _category.id pdbx_entity_src_gen_fract _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_fract.entry_id' '_pdbx_entity_src_gen_fract.entity_id' '_pdbx_entity_src_gen_fract.step_id' save_ save__pdbx_entity_src_gen_fract.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_fract.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_fract.entry_id' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_fract.entry_id' save_ save__pdbx_entity_src_gen_fract.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_fract.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_fract.entity_id' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_fract.entity_id' save_ save__pdbx_entity_src_gen_fract.step_id _item_description.description ; This item is the unique identifier for this fractionation step. ; _item.name '_pdbx_entity_src_gen_fract.step_id' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_fract.next_step_id _item_description.description ; This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. ; _item.name '_pdbx_entity_src_gen_fract.next_step_id' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_fract.end_construct_id _item_description.description ; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the fractionation step. ; _item.name '_pdbx_entity_src_gen_fract.end_construct_id' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code no _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_entity_src_gen_fract.end_construct_id' save_ save__pdbx_entity_src_gen_fract.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_fract.robot_id' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_fract.robot_id' save_ save__pdbx_entity_src_gen_fract.date _item_description.description ; The date of this production step. ; _item.name '_pdbx_entity_src_gen_fract.date' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_fract.method _item_description.description ; This item describes the method of fractionation. ; _item.name '_pdbx_entity_src_gen_fract.method' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail C 'Centrifugation' M 'Magnetic beads' P 'Phase separation' save_ save__pdbx_entity_src_gen_fract.temperature _item_description.description ; The temperature in degrees celsius at which the fractionation was performed. ; _item.name '_pdbx_entity_src_gen_fract.temperature' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_fract.details _item_description.description ; String value containing details of the fractionation. ; _item.name '_pdbx_entity_src_gen_fract.details' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_fract.protein_location _item_description.description ; The fraction containing the protein of interest. ; _item.name '_pdbx_entity_src_gen_fract.protein_location' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail S 'Supernatant' P 'Pellet' B 'Band in gradient' M 'Magnetic beads' A 'Aqueous phase' L 'Lipid phase' save_ save__pdbx_entity_src_gen_fract.protein_volume _item_description.description ; The volume of the fraction containing the protein. ; _item.name '_pdbx_entity_src_gen_fract.protein_volume' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code no _item_type.code float _item_units.code milliliters save_ save__pdbx_entity_src_gen_fract.protein_yield _item_description.description ; The yield in milligrams of protein from the fractionation. ; _item.name '_pdbx_entity_src_gen_fract.protein_yield' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_type.code float _item_units.code milligrams save_ save__pdbx_entity_src_gen_fract.protein_yield_method _item_description.description ; The method used to determine the yield ; _item.name '_pdbx_entity_src_gen_fract.protein_yield_method' _item.category_id pdbx_entity_src_gen_fract _item.mandatory_code yes _item_type.code text save_ ############################ # PDBX_ENTITY_SRC_GEN_PURE # ############################ # # _pdbx_entity_src_gen_pure.entry_id # _pdbx_entity_src_gen_pure.entity_id # _pdbx_entity_src_gen_pure.next_step_id # _pdbx_entity_src_gen_pure.date # _pdbx_entity_src_gen_pure.conc_device_id # _pdbx_entity_src_gen_pure.conc_details # _pdbx_entity_src_gen_pure.conc_assay_method # _pdbx_entity_src_gen_pure.protein_concentration # _pdbx_entity_src_gen_pure.protein_yield # _pdbx_entity_src_gen_pure.protein_purity # _pdbx_entity_src_gen_pure.protein_oligomeric_state # _pdbx_entity_src_gen_pure.storage_buffer_id # _pdbx_entity_src_gen_pure.storage_temperature # # _pdbx_entity_src_gen_pure.summary # save_pdbx_entity_src_gen_pure _category.description ; This category contains details for the final purified protein product. Note that this category does not contain the amino acid sequence of the protein. The sequence will be found in the ENTITY_POLY_SEQ entry with matching entity_id. Only one PDBX_ENTITY_SRC_GEN_PURE category is allowed per entity, hence there is no step_id for this category. ; _category.id pdbx_entity_src_gen_pure _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_pure.entry_id' '_pdbx_entity_src_gen_pure.entity_id' '_pdbx_entity_src_gen_pure.step_id' save_ save__pdbx_entity_src_gen_pure.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_pure.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_pure.entry_id' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_pure.entry_id' save_ save__pdbx_entity_src_gen_pure.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_pure.entity_id uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_pure.entity_id' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_pure.entity_id' save_ save__pdbx_entity_src_gen_pure.step_id _item_description.description ; This item unique identifier the production step. ; _item.name '_pdbx_entity_src_gen_pure.step_id' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_pure.product_id _item_description.description ; When present, this item should be a globally unique identifier that identifies the final product. It is envisaged that this should be the same as and product code associated with the sample and would provide the key by which information about the production process may be extracted from the protein production facility. For files describing the protein production process (i.e. where _entity.type is 'P' or 'E') this should have the same value as _entry.id ; _item.name '_pdbx_entity_src_gen_pure.product_id' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code code save_ save__pdbx_entity_src_gen_pure.date _item_description.description ; The date of production step. ; _item.name '_pdbx_entity_src_gen_pure.date' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_pure.conc_device_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_pure.conc_device_id' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_pure.conc_device_id' save_ save__pdbx_entity_src_gen_pure.conc_details _item_description.description ; Details of the protein concentration procedure ; _item.name '_pdbx_entity_src_gen_pure.conc_details' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code text save_ save__pdbx_entity_src_gen_pure.conc_assay_method _item_description.description ; The method used to measure the protein concentration ; _item.name '_pdbx_entity_src_gen_pure.conc_assay_method' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_pure.protein_concentration _item_description.description ; The final concentration of the protein. ; _item.name '_pdbx_entity_src_gen_pure.protein_concentration' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code yes _item_type.code float _item_units.code mg_per_ml save_ save__pdbx_entity_src_gen_pure.protein_yield _item_description.description ; The yield of protein in milligrams. ; _item.name '_pdbx_entity_src_gen_pure.protein_yield' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code float _item_units.code milligrams save_ save__pdbx_entity_src_gen_pure.protein_purity _item_description.description ; The purity of the protein (percent). ; _item.name '_pdbx_entity_src_gen_pure.protein_purity' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code float # _item_units.code percent save_ save__pdbx_entity_src_gen_pure.protein_oligomeric_state _item_description.description ; The oligomeric state of the protein. Monomeric is 1, dimeric 2, etc. ; _item.name '_pdbx_entity_src_gen_pure.protein_oligomeric_state' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code int save_ save__pdbx_entity_src_gen_pure.storage_buffer_id _item_description.description ; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was stored. ; _item.name '_pdbx_entity_src_gen_pure.storage_buffer_id' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code yes _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_entity_src_gen_pure.storage_buffer_id' save_ save__pdbx_entity_src_gen_pure.storage_temperature _item_description.description ; The temperature in degrees celsius at which the protein was stored. ; _item.name '_pdbx_entity_src_gen_pure.storage_temperature' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code float _item_units.code celsius save_ save__pdbx_entity_src_gen_pure.summary _item_description.description ; Summary of the details of protein purification method used to obtain the final protein product. This description should include any lysis, fractionation, proteolysis, refolding, chromatography used as well as the method used the characterize the final product. ; _item.name '_pdbx_entity_src_gen_pure.summary' _item.category_id pdbx_entity_src_gen_pure _item.mandatory_code no _item_type.code text save_ ################################# # PDBX_ENTITY_SRC_GEN_CHARACTER # ################################# # # _pdbx_entity_src_gen_character.entry_id # _pdbx_entity_src_gen_character.entity_id # _pdbx_entity_src_gen_character.step_id # _pdbx_entity_src_gen_character.robot_id # _pdbx_entity_src_gen_character.date # _pdbx_entity_src_gen_character.method # _pdbx_entity_src_gen_character.value # _pdbx_entity_src_gen_character.details # save_pdbx_entity_src_gen_character _category.description ; This category contains details of protein characterisation. It refers to the characteristion of the product of a specific step. ; _category.id pdbx_entity_src_gen_character _category.mandatory_code no loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'entity_group' 'pdbx_group' loop_ _category_key.name '_pdbx_entity_src_gen_character.entry_id' '_pdbx_entity_src_gen_character.entity_id' '_pdbx_entity_src_gen_character.step_id' save_ save__pdbx_entity_src_gen_character.entry_id _item_description.description ; The value of _pdbx_entity_src_gen_character.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_character.entry_id' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_entity_src_gen_character.entry_id' save_ save__pdbx_entity_src_gen_character.entity_id _item_description.description ; The value of _pdbx_entity_src_gen_character.entity_id uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code. ; _item.name '_pdbx_entity_src_gen_character.entity_id' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code yes _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_entity_src_gen_character.entity_id' save_ save__pdbx_entity_src_gen_character.step_id _item_description.description ; This item is the unique identifier for the step whose product has been characterised. ; _item.name '_pdbx_entity_src_gen_character.step_id' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code yes _item_type.code int save_ save__pdbx_entity_src_gen_character.robot_id _item_description.description ; This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. ; _item.name '_pdbx_entity_src_gen_character.robot_id' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_entity_src_gen_character.robot_id' save_ save__pdbx_entity_src_gen_character.date _item_description.description ; The date of characterisation step. ; _item.name '_pdbx_entity_src_gen_character.date' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_entity_src_gen_character.method _item_description.description ; The method used for protein characterisation. ; _item.name '_pdbx_entity_src_gen_character.method' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'Dynamic light scattering' 'Mass spectrometry' save_ save__pdbx_entity_src_gen_character.result _item_description.description ; The result from this method of protein characterisation. ; _item.name '_pdbx_entity_src_gen_character.result' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code yes _item_type.code text save_ save__pdbx_entity_src_gen_character.details _item_description.description ; Any details associated with this method of protein characterisation. ; _item.name '_pdbx_entity_src_gen_character.details' _item.category_id pdbx_entity_src_gen_character _item.mandatory_code no _item_type.code text save_ ################## # PDBX_CONSTRUCT # ################## # # _pdbx_construct.entry_id # _pdbx_construct.id # _pdbx_construct.name # _pdbx_construct.class # _pdbx_construct.type # _pdbx_construct.seq # _pdbx_construct.date # _pdbx_construct.details # _pdbx_construct.robot_id # _pdbx_construct.ref_db_code # _pdbx_construct.ref_db_name # _pdbx_construct.ref_db_align_beg # _pdbx_construct.ref_db_align_end # _pdbx_construct.flag_align # _pdbx_construct.flag_diff # save_pdbx_construct _category.description ; Data items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids. It is a catch-all that may be used to provide details of sequences known to be relevant to the project as well as primers, plasmids, proteins and such like that are either used or produced during the protein production process. Molecules described here are not necessarily complete, so for instance it would be possible to include either a complete plasmid or just its insert. This category may be considered as an abbreviated form of _entity where the molecules described are not required to appear in the final co-ordinates. Note that the details provided here all pertain to a single entry as defined at deposition. It is anticipated that _pdbx_construct.id would also be composed of a sequence that is unique within a given site prefixed by a code that identifies that site and would, therefore, be GLOBALLY unique. Thus this category could also be used locally to store details about the different constructs used during protein production without reference to the entry_id (which only becomes a meaningful concept during deposition). ; _category.id pdbx_construct _category.mandatory_code no loop_ _category_key.name '_pdbx_construct.id' loop_ _category_group.id 'inclusive_group' 'entity_group' 'protein_production_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example ; ; _pdbx_construct.entry_id 111000111 _pdbx_construct.id 1 _pdbx_construct.type DNA _pdbx_construct.entity_id 1 _pdbx_construct.seq ; gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg # - - - - data truncated for brevity - - - - ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_construct.entry_id _item_description.description ; The value of _pdbx_construct.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_construct.entry_id' _item.category_id pdbx_construct _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_construct.entry_id' save_ save__pdbx_construct.id _item_description.description ; The value of _pdbx_construct.id must uniquely identify a record in the PDBX_CONSTRUCT list and should be arranged so that it is composed of a site-speicific prefix combined with a value that is unique within a given site.Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name '_pdbx_construct.id' _item.category_id pdbx_construct _item.mandatory_code yes _item_type.code code save_ save__pdbx_construct.name _item_description.description ; _pdbx_construct.name provides a placeholder for the local name of the construct, for example the plasmid name if this category is used to list plasmids. ; loop_ _item.name '_pdbx_construct.name' _item.category_id pdbx_construct _item.mandatory_code yes _item_type.code line save_ save__pdbx_construct.organisation _item_description.description ; _pdbx_construct.organisation describes the organisation in which the _pdbx_construct.id is unique. This will normally be the lab in which the constrcut originated. It is envisaged that this item will permit a globally unique identifier to be constructed in cases where this is not possible from the _pdbx_construct.id alone. ; loop_ _item.name '_pdbx_construct.organisation' _item.category_id pdbx_construct _item.mandatory_code yes _item_type.code line save_ save__pdbx_construct.entity_id _item_description.description ; In cases where the construct IS found in the co-ordinates then this item provides a pointer to _entity.id in the ENTITY category for the corresponding molecule. ; _item.name '_pdbx_construct.entity_id' _item.category_id pdbx_construct _item.mandatory_code no _item_linked.parent_name '_entity.id' _item_linked.child_name '_pdbx_construct.entity_id' save_ save__pdbx_construct.robot_id _item_description.description ; In cases where the sequence has been determined by a robot this data item provides a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category for the robot responsible ; _item.name '_pdbx_construct.robot_id' _item.category_id pdbx_construct _item.mandatory_code no _item_linked.parent_name '_pdbx_robot_system.id' _item_linked.child_name '_pdbx_construct.robot_id' save_ save__pdbx_construct.date _item_description.description ; The date that the sequence was determined. ; _item.name '_pdbx_construct.date' _item.category_id pdbx_construct _item.mandatory_code no _item_type.code yyyy-mm-dd:hh:mm loop_ _item_examples.case '2003-12-25' '2003-12-25:09:00' save_ save__pdbx_construct.details _item_description.description ; Additional details about the construct that cannot be represented in the category _pdbx_construct_feature. ; _item.name '_pdbx_construct.details' _item.category_id pdbx_construct _item.mandatory_code no _item_type.code text save_ save__pdbx_construct.class _item_description.description ; The primary function of the construct. This should be considered as a guideline only. ; _item.name '_pdbx_construct.class' _item.category_id pdbx_construct _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value plasmid protein insert primer transcript save_ save__pdbx_construct.type _item_description.description ; The type of nucleic acid sequence in the construct. Note that to find all the DNA molecules it is necessary to search for DNA + cDNA and for RNA, RNA + mRNA + tRNA. ; _item.name '_pdbx_construct.type' _item.category_id pdbx_construct _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value DNA RNA cDNA mRNA tRNA protein save_ save__pdbx_construct.seq _item_description.description ; sequence expressed as string of one-letter base codes or one letter amino acid codes. Unusual residues may be represented either using the appropriate one letter code wild cards or by the three letter code in parentheses. ; _item.name '_pdbx_construct.seq' _item.category_id pdbx_construct _item.mandatory_code yes _item_type.code text _item_examples.case ; gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg ; save_ ########################### # PDBX_CONSTRUCT_FEATURE # ########################### # # _pdbx_construct_feature.id # _pdbx_construct_feature.entry_id # _pdbx_construct_feature.entity_id # _pdbx_construct_feature.construct_id # _pdbx_construct_feature.start_seq # _pdbx_construct_feature.end_seq # _pdbx_construct_feature.type # _pdbx_construct_feature.details # save_pdbx_construct_feature _category.description ; Data items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production. ; _category.id pdbx_construct_feature _category.mandatory_code no loop_ _category_key.name '_pdbx_construct_feature.construct_id' '_pdbx_construct_feature.id' loop_ _category_group.id 'inclusive_group' 'entity_group' 'protein_production_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - vector pUC28 ; ; loop_ _pdbx_construct_feature.id _pdbx_construct_feature.entry_id _pdbx_construct_feature.construct_id _pdbx_construct_feature.start_seq _pdbx_construct_feature.end_seq _pdbx_construct_feature.type _pdbx_construct_feature.details 1 111000111 1 . . . "pKK84-1 ClaI 5260bp 5247..5247 ptac11 TaqI-TaqI 192bp, -35 trp promoter -> pEA300 5452bp" 2 111000111 1 . . . "pKK84-1 1..5246 5246bp ClaI = AT^CGAT TaqI = T^CGA cgact..." 3 111000111 1 5247 5436 . "ptac11 190bp ...cat TaqI = T^CGA ClaI = AT^CGAT" 4 111000111 1 5437 5450 . "pKK84-1 5247..5260 14bp" 5 111000111 1 . . misc_binding "SIT unique EcoRI-ClaI-HindIII-BamHI-PvuII" 6 111000111 1 . . rep_origin "ORI E. coli pMB1 (ColE1 and pBR322)" 7 111000111 1 . . promoter "PRO E. coli trp" 8 111000111 1 . . CDS "ANT E. coli beta-lactamase gene (bla) ampicillin resistance gene (apr/amp)" ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_construct_feature.id _item_description.description ; The value of _pdbx_construct_feature.id must uniquely identify a record in the PDBX_CONSTRUCT_FEATURE list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name '_pdbx_construct_feature.id' _item.category_id pdbx_construct_feature _item.mandatory_code yes _item_type.code code save_ save__pdbx_construct_feature.construct_id _item_description.description ; The value of _pdbx_construct_feature.construct_id uniquely identifies the construct with which the feature is associated. This is a pointer to _pdbx_construct.id This item may be a site dependent bar code. ; _item.name '_pdbx_construct_feature.construct_id' _item.category_id pdbx_construct_feature _item.mandatory_code yes _item_linked.parent_name '_pdbx_construct.id' _item_linked.child_name '_pdbx_construct_feature.construct_id' save_ save__pdbx_construct_feature.entry_id _item_description.description ; The value of _pdbx_construct_feature.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code. ; _item.name '_pdbx_construct_feature.entry_id' _item.category_id pdbx_construct _item.mandatory_code yes _item_linked.parent_name '_entry.id' _item_linked.child_name '_pdbx_construct_feature.entry_id' save_ save__pdbx_construct_feature.start_seq _item_description.description ; The sequence position at which the feature begins ; _item.name '_pdbx_construct_feature.start_seq' _item.category_id pdbx_construct_feature _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__pdbx_construct_feature.end_seq _item_description.description ; The sequence position at which the feature ends ; _item.name '_pdbx_construct_feature.end_seq' _item.category_id pdbx_construct_feature _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__pdbx_construct_feature.type _item_description.description ; The type of the feature ; _item.name '_pdbx_construct_feature.type' _item.category_id pdbx_construct_feature _item.mandatory_code no _item_type.code line save_ save__pdbx_construct_feature.details _item_description.description ; Details that describe the feature ; _item.name '_pdbx_construct_feature.details' _item.category_id pdbx_construct_feature _item.mandatory_code no _item_type.code text save_ ##################### # PDBX_ROBOT_SYSTEM # ##################### # # _pdbx_robot_system.id # _pdbx_robot_system.model # _pdbx_robot_system.type # _pdbx_robot_system.manufacturer # save_pdbx_robot_system _category.description ; The details about each robotic system used to collect data for this project. ; _category.id pdbx_robot_system _category.mandatory_code no _category_key.name '_pdbx_robot_system.id' loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'pdbx_group' save_ save__pdbx_robot_system.id _item_description.description ; Assign a numerical ID to each instrument. ; _item.name '_pdbx_robot_system.id' _item.category_id pdbx_robot_system _item.mandatory_code no _item_type.code code save_ save__pdbx_robot_system.model _item_description.description ; The model of the robotic system. ; _item.name '_pdbx_robot_system.model' _item.category_id pdbx_robot_system _item.mandatory_code no _item_type.code line save_ save__pdbx_robot_system.type _item_description.description ; The type of robotic system used for in the production pathway. ; _item.name '_pdbx_robot_system.type' _item.category_id pdbx_robot_system _item.mandatory_code no _item_type.code line save_ save__pdbx_robot_system.manufacturer _item_description.description ; The name of the manufacturer of the robotic system. ; _item.name '_pdbx_robot_system.manufacturer' _item.category_id pdbx_robot_system _item.mandatory_code no _item_type.code line save_ ################# ## PDB_BUFFER ## ################# # # _pdbx_buffer.id # _pdbx_buffer.name # _pdbx_buffer.details # _pdbx_buffer_components.id # _pdbx_buffer_components.buffer_id # _pdbx_buffer_components.name # _pdbx_buffer_components.volume # _pdbx_buffer_components.conc # _pdbx_buffer_components.details # _pdbx_buffer_components.conc_units # _pdbx_buffer_components.isotopic_labeling # save_pdbx_buffer _category.description ; Data items in the PDBX_BUFFER category record details of the sample buffer. ; _category.id pdbx_buffer _category.mandatory_code no _category_key.name '_pdbx_buffer.id' loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'pdbx_group' save_ save__pdbx_buffer.id _item_description.description ; The value of _pdbx_buffer.id must uniquely identify the sample buffer. ; _item.name '_pdbx_buffer.id' _item.category_id pdbx_buffer _item.mandatory_code yes _item_type.code code save_ save__pdbx_buffer.name _item_description.description ; The name of each buffer. ; _item.name '_pdbx_buffer.name' _item.category_id pdbx_buffer _item.mandatory_code no _item_type.code line _item_examples.case 'Acetic acid' save_ save__pdbx_buffer.details _item_description.description ; Any additional details to do with buffer. ; _item.name '_pdbx_buffer.details' _item.category_id pdbx_buffer _item.mandatory_code no _item_type.code text _item_examples.case 'aerated' save_ ############################### ## PDBX_BUFFER_COMPONENTS ## ############################### # # _pdbx_buffer_components.id # _pdbx_buffer_components.buffer_id # _pdbx_buffer_components.name # _pdbx_buffer_components.volume # _pdbx_buffer_components.conc # _pdbx_buffer_components.details # _pdbx_buffer_components.conc_units # _pdbx_buffer_components.isotopic_labeling # save_pdbx_buffer_components _category.description ; Constituents of buffer in sample ; _category.id pdbx_buffer_components _category.mandatory_code no loop_ _category_key.name '_pdbx_buffer_components.buffer_id' '_pdbx_buffer_components.id' loop_ _category_group.id 'inclusive_group' 'protein_production_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ;loop_ _pdbx_buffer_components.buffer_id _pdbx_buffer_components.id _pdbx_buffer_components.name _pdbx_buffer_components.volume _pdbx_buffer_components.conc _pdbx_buffer_components.details 1 1 'NaCl' '0.200 ' '4 ' . 1 2 'Acetic Acid' '0.047 ' '100' . 1 3 'water' '0.700 ' 'neat' . ; save_ save__pdbx_buffer_components.id _item_description.description ; The value of _pdbx_buffer_components.id must uniquely identify a component of the buffer. ; _item.name '_pdbx_buffer_components.id' _item.category_id pdbx_buffer_components _item.mandatory_code yes _item_type.code code save_ save__pdbx_buffer_components.buffer_id _item_description.description ; This data item is a pointer to _pdbx_buffer.id in the BUFFER category. ; _item.name '_pdbx_buffer_components.buffer_id' _item.category_id pdbx_buffer_components _item.mandatory_code yes _item_linked.parent_name '_pdbx_buffer.id' _item_linked.child_name '_pdbx_buffer_components.buffer_id' save_ save__pdbx_buffer_components.name _item_description.description ; The name of each buffer component. ; _item.name '_pdbx_buffer_components.name' _item.category_id pdbx_buffer_components _item.mandatory_code no _item_type.code line _item_examples.case 'Acetic acid' save_ save__pdbx_buffer_components.volume _item_description.description ; The volume of buffer component. ; _item.name '_pdbx_buffer_components.volume' _item.category_id pdbx_buffer_components _item.mandatory_code no _item_type.code code _item_examples.case 0.200 save_ save__pdbx_buffer_components.conc _item_description.description ; The millimolar concentration of buffer component. ; _item.name '_pdbx_buffer_components.conc' _item.category_id pdbx_buffer_components _item.mandatory_code no _item_type.code code _item_examples.case 200 save_ save__pdbx_buffer_components.details _item_description.description ; Any additional details to do with buffer composition. ; _item.name '_pdbx_buffer_components.details' _item.category_id pdbx_buffer_components _item.mandatory_code no _item_type.code text _item_examples.case 'pH adjusted with NaOH' save_ # save__pdbx_buffer_components.conc_units _item_description.description ; The concentration units of the component. ; _item.name '_pdbx_buffer_components.conc_units' _item.category_id pdbx_buffer_components _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'mg/mL for mg per milliliter' 'mM for millimolar' '% for percent by volume' loop_ _item_enumeration.value _item_enumeration.detail '%' 'percent by volume' 'mM' 'millimolar' 'mg/mL' 'mg per milliliter' 'M' 'molar' 'g/L' 'grams per liter' save_ save__pdbx_buffer_components.isotopic_labeling _item_description.description ; The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H ; _item.name '_pdbx_buffer_components.isotopic_labeling' _item.category_id pdbx_buffer_components _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'U-15N' 'U-13C' 'U-15N,13C' 'U-2H' 'other' save_ ### EOF mmcif_pdbx-def-6.dic ########################################################################### # # File: mmcif_iims-def-2.dic # # PDB Extension Dictionary for 3-Dimensional # Electron Microscopy # # Definition Section 2 # # ########################################################################### ## ### # Please note the data items listed below are not for the PDB # but are intended solely for the EM database # _em_entity_assembly.ebi_organism_scientific # _em_entity_assembly.ebi_organism_common # _em_entity_assembly.ebi_strain # _em_entity_assembly.ebi_tissue # _em_entity_assembly.ebi_cell # _em_entity_assembly.ebi_organelle # _em_entity_assembly.ebi_cellular_location # _em_entity_assembly.ebi_engineered # _em_entity_assembly.ebi_expression_system # _em_entity_assembly.ebi_expression_system_plasmid ### # # categories # # EM_ASSEMBLY # _em_assembly.id # _em_assembly.entry_id # _em_assembly.name # _em_assembly.aggregation_state # _em_assembly.composition # _em_assembly.num_components # _em_assembly.mol_wt_exp # _em_assembly.mol_wt_theo # _em_assembly.mol_wt_method # _em_assembly.details # EM_ENTITY_ASSEMBLY # _em_entity_assembly.id # _em_entity_assembly.assembly_id # _em_entity_assembly.type # _em_entity_assembly.name # _em_entity_assembly.details # _em_entity_assembly.go_id # _em_entity_assembly.ipr_id # _em_entity_assembly.synonym # EM_ENTITY_ASSEMBLY_LIST # _em_entity_assembly_list.id # _em_entity_assembly_list.entity_id # _em_entity_assembly_list.entity_assembly_id # _em_entity_assembly_list.oligomeric_details # _em_entity_assembly_list.number_of_copies # EM_VIRUS_ENTITY # _em_virus_entity.id # _em_virus_entity.virus_host_category # _em_virus_entity.virus_host_species # _em_virus_entity.virus_host_growth_cell # _em_virus_entity.virus_type # _em_virus_entity.virus_isolate # _em_virus_entity.ictvdb_id # _em_virus_entity.entity_assembly_id # _em_virus_entity.enveloped # _em_virus_entity.empty # EM_ICOS_VIRUS_SHELLS # _em_icos_virus_shells.virus_entity_id # _em_icos_virus_shells.id # _em_icos_virus_shells.shell_diameter # _em_icos_virus_shells.triangulation_num # EM_SAMPLE_PREPARATION # _em_sample_preparation.entry_id # _em_sample_preparation.id # _em_sample_preparation.ph # _em_sample_preparation.buffer_id # _em_sample_preparation.sample_concentration # _em_sample_preparation.2d_crystal_grow_id # _em_sample_preparation.support_id # EM_SAMPLE_SUPPORT # _em_sample_support.id # _em_sample_support.film_material # _em_sample_support.method # _em_sample_support.grid_material # _em_sample_support.grid_mesh_size # _em_sample_support.grid_type # _em_sample_support.pretreatment # _em_sample_support.details # _em_sample_support.citation_id # EM_2D_CRYSTAL_GROW # _em_2d_crystal_grow.id # _em_2d_crystal_grow.method # _em_2d_crystal_grow.apparatus # _em_2d_crystal_grow.atmosphere # _em_2d_crystal_grow.pH # _em_2d_crystal_grow.temp # _em_2d_crystal_grow.time # _em_2d_crystal_grow.buffer_id # _em_2d_crystal_grow.details # _em_2d_crystal_grow.number_2d_crystals # _em_2d_crystal_grow.mean_2d_crystal_size # _em_2d_crystal_grow.citation_id # EM_BUFFER # _em_buffer.id # _em_buffer.name # _em_buffer.details # EM_BUFFER_COMPONENTS # _em_buffer_components.id # _em_buffer_components.buffer_id # _em_buffer_components.name # _em_buffer_components.volume # _em_buffer_components.conc # _em_buffer_components.details # EM_VITRIFICATION # _em_vitrification.entry_id # _em_vitrification.id # _em_vitrification.sample_preparation_id # _em_vitrification.cryogen_name # _em_vitrification.humidity # _em_vitrification.temp # _em_vitrification.instrument # _em_vitrification.method # _em_vitrification.time_resolved_state # _em_vitrification.citation_id # _em_vitrification.details # EM_IMAGING # _em_imaging.entry_id # _em_imaging.id # _em_imaging.sample_support_id # _em_imaging.detector_id # _em_imaging.scans_id # _em_imaging.microscope_model # _em_imaging.specimen_holder_type # _em_imaging.specimen_holder_model # _em_imaging.details # _em_imaging.date # _em_imaging.accelerating_voltage # _em_imaging.illumination_mode # _em_imaging.mode # _em_imaging.nominal_cs # _em_imaging.nominal_defocus_min # _em_imaging.nominal_defocus_max # _em_imaging.tilt_angle_min # _em_imaging.tilt_angle_max # _em_imaging.nominal_magnification # _em_imaging.calibrated_magnification # _em_imaging.electron_source # _em_imaging.electron_dose # _em_imaging.energy_filter # _em_imaging.energy_window # _em_imaging.citation_id # _em_imaging.temperature # _em_imaging.detector_distance # _em_imaging.recording_temperature_minimum # _em_imaging.recording_temperature_maximum # EM_DETECTOR # _em_detector.entry_id # _em_detector.id # _em_detector.details # _em_detector.type # _em_detector.detective_quantum_efficiency # EM_IMAGE_SCANS # _em_image_scans.entry_id # _em_image_scans.id # _em_image_scans.number_digital_images # _em_image_scans.details # _em_image_scans.scanner_model # _em_image_scans.sampling_size # _em_image_scans.od_range # _em_image_scans.quant_bit_size # _em_image_scans.citation_id # EM_2D_PROJECTION_SELECTION # _em_2d_projection_selection.entry_id # _em_2d_projection_selection.num_particles # _em_2d_projection_selection.software_name # _em_2d_projection_selection.method # _em_2d_projection_selection.details # _em_2d_projection_selection.citation_id # EM_EULER_ANGLE_DISTRIBUTION # _em_euler_angle_distribution.id # _em_euler_angle_distribution.entry_id # _em_euler_angle_distribution.details # _em_euler_angle_distribution.alpha # _em_euler_angle_distribution.beta # _em_euler_angle_distribution.gamma # EM_3D_RECONSTRUCTION # _em_3d_reconstruction.entry_id # _em_3d_reconstruction.id # _em_3d_reconstruction.method # _em_3d_reconstruction.citation_id # _em_3d_reconstruction.details # _em_3d_reconstruction.resolution # _em_3d_reconstruction.resolution_method # _em_3d_reconstruction.magnification_calibration # _em_3d_reconstruction.ctf_correction_method # _em_3d_reconstruction.nominal_pixel_size # _em_3d_reconstruction.actual_pixel_size # EM_3D_FITTING # _em_3d_fitting.id # _em_3d_fitting.entry_id # _em_3d_fitting.method # _em_3d_fitting.target_criteria # _em_3d_fitting.software_name # _em_3d_fitting.details # _em_3d_fitting.overall_b_value # _em_3d_fitting.ref_space # _em_3d_fitting.ref_protocol # EM_3D_FITTING_LIST # _em_3d_fitting_list.id # _em_3d_fitting_list.3d_fitting_id # _em_3d_fitting_list.pdb_entry_id # _em_3d_fitting_list.pdb_chain_id ################# ## EM_ASSEMBLY ## ################# save_em_assembly _category.description ; Data items in the EM_ASSEMBLY category record details about the type of complex assembly that describes the nature of the sample studied. ; _category.id em_assembly _category.mandatory_code no loop_ _category_key.name '_em_assembly.id' '_em_assembly.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_assembly.id 1 _em_assembly.entry_id 1DYL _em_assembly.name virus _em_assembly.aggregation_state icosahedral _em_assembly.composition virus _em_assembly.num_components 1 _em_assembly.mol_wt_exp . _em_assembly.mol_wt_theo . _em_assembly.mol_wt_method . _em_assembly.details . ; save_ save__em_assembly.id _item_description.description ; The value of _em_assembly.id must uniquely identify a collection of observed complexes. ; _item.name '_em_assembly.id' _item.category_id em_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly.assembly_id' _item_linked.parent_name '_em_assembly.id' save_ save__em_assembly.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_assembly.entry_id' _item.category_id em_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_assembly.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_assembly.name _item_description.description ; The name of the assembly of observed complexes. ; _item.name '_em_assembly.name' _item.category_id em_assembly _item.mandatory_code no _item_type.code line save_ save__em_assembly.aggregation_state _item_description.description ; A description of the aggregation state of the assembly. ; _item.name '_em_assembly.aggregation_state' _item.category_id em_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'SINGLE PARTICLE' 'INDIVIDUAL STRUCTURE' '2D-CRYSTAL' ICOSAHEDRAL HELICAL FILAMENT 'HELICAL FILAMENTS' TISSUE save_ save__em_assembly.composition _item_description.description ; The known composition of the assembly. ; _item.name '_em_assembly.composition' _item.category_id em_assembly _item.mandatory_code no _item_type.code line save_ save__em_assembly.num_components _item_description.description ; The number of components of the biological assembly. ; _item.name '_em_assembly.num_components' _item.category_id em_assembly _item.mandatory_code no _item_type.code int save_ save__em_assembly.mol_wt_exp _item_description.description ; The value (in megadaltons) of the experimentally determined molecular weight of the assembly. ; _item.name '_em_assembly.mol_wt_exp' _item.category_id em_assembly _item.mandatory_code no _item_type.code float _item_units.code megadaltons save_ save__em_assembly.mol_wt_theo _item_description.description ; The value (in megadaltons) of the theoretically determined molecular weight of the assembly. ; _item.name '_em_assembly.mol_wt_theo' _item.category_id em_assembly _item.mandatory_code no _item_type.code float _item_units.code megadaltons save_ save__em_assembly.mol_wt_method _item_description.description ; The method used in determining the molecular weight. ; _item.name '_em_assembly.mol_wt_method' _item.category_id em_assembly _item.mandatory_code no _item_type.code text save_ save__em_assembly.details _item_description.description ; A description of any additional details describing the observed sample. ; _item.name '_em_assembly.details' _item.category_id em_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; This structure was preferentially oriented (end-on)on the grid. ; ; The structure was monodisperse. ; save_ ######################## ## EM_ENTITY_ASSEMBLY ## ######################## save_em_entity_assembly _category.description ; Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. ; _category.id em_entity_assembly _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly.id' '_em_entity_assembly.assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_entity_assembly.id 1 _em_entity_assembly.assembly_id 1 _em_entity_assembly.type VIRUS ; save_ save__em_entity_assembly.id _item_description.description ; The value of _em_entity_assembly.id must uniquely identify each of the components of the complex. ; _item.name '_em_entity_assembly.id' _item.category_id em_entity_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_virus_entity.entity_assembly_id' _item_linked.parent_name '_em_entity_assembly.id' save_ save__em_entity_assembly.assembly_id _item_description.description ; This data item is a pointer to _em_assembly.id in the ASSEMBLY category. ; _item.name '_em_entity_assembly.assembly_id' _item.category_id em_entity_assembly _item.mandatory_code yes _item_type.code code save_ save__em_entity_assembly.type _item_description.description ; A description of types of components of the assembly of the biological structure. ; _item.name '_em_entity_assembly.type' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value VIRUS PROTEIN 'NUCLEIC ACID' LIGAND LABEL 'CELLULAR COMPONENT' save_ save__em_entity_assembly.name _item_description.description ; The name of the component of the observed assembly. ; _item.name '_em_entity_assembly.name' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.details _item_description.description ; Additional details about the component. ; _item.name '_em_entity_assembly.details' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.ebi_organism_scientific _item_description.description ; The species of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_organism_scientific' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.ebi_organism_common _item_description.description ; The common name of the species of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_organism_common' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text save_ save__em_entity_assembly.ebi_strain _item_description.description ; The strain of the natural organism from which the component was obtained, if relevant. ; _item.name '_em_entity_assembly.ebi_strain' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__em_entity_assembly.ebi_tissue _item_description.description ; The tissue of the natural organism from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_tissue' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' save_ save__em_entity_assembly.ebi_cell _item_description.description ; The cell from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_cell' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CHO' 'HELA' '3T3' save_ save__em_entity_assembly.ebi_organelle _item_description.description ; The organelle from which the component was obtained. ; _item.name '_em_entity_assembly.ebi_organelle' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'golgi' 'mitochondrion' 'cytoskeleton' save_ save__em_entity_assembly.ebi_cellular_location _item_description.description ; The cellular location of the component. ; _item.name '_em_entity_assembly.ebi_cellular_location' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'cytoplasm' 'endoplasmic reticulum' 'plasma membrane' save_ save__em_entity_assembly.ebi_engineered _item_description.description ; A flag to indicate whether the component is engineered. ; _item.name '_em_entity_assembly.ebi_engineered' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ save__em_entity_assembly.ebi_expression_system _item_description.description ; The expression system used to produce the component. ; _item.name '_em_entity_assembly.ebi_expression_system' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'eschericia coli' 'saccharomyces cerevisiae' save_ save__em_entity_assembly.ebi_expression_system_plasmid _item_description.description ; The plasmid used in the expression system used to produce the component. ; _item.name '_em_entity_assembly.ebi_expression_system_plasmid' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'pBR322' 'pMB9' save_ save__em_entity_assembly.go_id _item_description.description ; The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). ; _item.name '_em_entity_assembly.go_id' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'GO:0005876' 'GO:0015630' save_ save__em_entity_assembly.ipr_id _item_description.description ; The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). ; _item.name '_em_entity_assembly.ipr_id' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line loop_ _item_examples.case '001304' '002353' save_ save__em_entity_assembly.synonym _item_description.description ; Alternative name of the component. ; _item.name '_em_entity_assembly.synonym' _item.category_id em_entity_assembly _item.mandatory_code no _item_type.code line _item_examples.case 'FADV-1' save_ ############################# ## EM_ENTITY_ASSEMBLY_LIST ## ############################# save_em_entity_assembly_list _category.description ; Data items in the EM_ENTITY_ASSEMBLY_LIST category record details of the structural elements in each component. ; _category.id em_entity_assembly_list _category.mandatory_code no loop_ _category_key.name '_em_entity_assembly_list.entity_assembly_id' '_em_entity_assembly_list.id' '_em_entity_assembly_list.entity_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - microtubule ; ; loop_ _em_entity_assembly_list.entity_assembly_id _em_entity_assembly_list.id _em_entity_assembly_list.entity_id _em_entity_assembly_list.oligomeric_details _em_entity_assembly_list.number_of_copies 1 1 1 'DIMER' 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_entity_assembly_list.id _item_description.description ; The value of _em_entity_assembly_list.id must uniquely identify the component. ; _item.name '_em_entity_assembly_list.id' _item.category_id em_entity_assembly_list _item.mandatory_code yes _item_type.code code save_ save__em_entity_assembly_list.entity_id _item_description.description ; A pointer to entity id. ; _item.name '_em_entity_assembly_list.entity_id' _item.category_id em_entity_assembly_list _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_entity_assembly_list.entity_id' _item_linked.parent_name '_entity.id' save_ save__em_entity_assembly_list.entity_assembly_id _item_description.description ; This data item is a pointer to _em_entity_assembly.id in the ENTITY_ASSEMBLY category. ; _item.name '_em_entity_assembly_list.entity_assembly_id' _item.category_id em_entity_assembly_list _item.mandatory_code yes _item_type.code code save_ save__em_entity_assembly_list.oligomeric_details _item_description.description ; The oligomeric state of the entity. ; _item.name '_em_entity_assembly_list.oligomeric_details' _item.category_id em_entity_assembly_list _item.mandatory_code no _item_type.code line save_ save__em_entity_assembly_list.number_of_copies _item_description.description ; The number of copies of the entity. ; _item.name '_em_entity_assembly_list.number_of_copies' _item.category_id em_entity_assembly_list _item.mandatory_code no _item_type.code int save_ ##################### ## EM_VIRUS_ENTITY ## ##################### save_em_virus_entity _category.description ; Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. ; _category.id em_virus_entity _category.mandatory_code no loop_ _category_key.name '_em_virus_entity.id' '_em_virus_entity.entity_assembly_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; loop_ _em_virus_entity.id _em_virus_entity.virus_host_category _em_virus_entity.virus_host_species _em_virus_entity.virus_type _em_virus_entity.virus_isolate _em_virus_entity.ictvdb_id _em_virus_entity.entity_assembly_id _em_virus_entity.enveloped _em_virus_entity.empty 1 'VERTERBRATES' 'HOMO SAPIENS' 'VIRUS' 'STRAIN' '00.073.0.01.023' 1 'YES' 'NO' ; save_ save__em_virus_entity.id _item_description.description ; Is the unique identifier for VIRUS_ENTITY category. ; _item.name '_em_virus_entity.id' _item.category_id em_virus_entity _item.mandatory_code yes _item_type.code code save_ save__em_virus_entity.virus_host_category _item_description.description ; The host category description for the virus. ; _item.name '_em_virus_entity.virus_host_category' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case ALGAE ARCHAEA 'BACTERIA(EUBACTERIA)' FUNGI INVERTEBRATES 'PLANTAE (HIGHER PLANTS)' PROTOZOA VERTEBRATES save_ save__em_virus_entity.virus_host_species _item_description.description ; The host species from which the virus was isolated. ; _item.name '_em_virus_entity.virus_host_species' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'homo sapiens' 'gallus gallus' save_ save__em_virus_entity.virus_host_growth_cell _item_description.description ; The host cell from which the virus was isolated. ; _item.name '_em_virus_entity.virus_host_growth_cell' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'HELA' 'CHO' save_ save__em_virus_entity.virus_type _item_description.description ; The type of virus. ; _item.name '_em_virus_entity.virus_type' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case VIRION SATELLITE PRION VIROID 'VIRUS-LIKE PARTICLE' save_ save__em_virus_entity.virus_isolate _item_description.description ; The isolate from which the virus was obtained. ; _item.name '_em_virus_entity.virus_isolate' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value STRAIN SEROTYPE SEROCOMPLEX SUBSPECIES SPECIES save_ save__em_virus_entity.ictvdb_id _item_description.description ; The International Committee on Taxonomy of Viruses (ICTV) Taxon Identifier is the Virus Code used throughout the ICTV database (ICTVdb). The ICTVdb id is the appropriate identifier used by the International Committee on Taxonomy of Viruses Resource. Reference: Virus Taxonomy, Academic Press (1999). ISBN:0123702003. ; _item.name '_em_virus_entity.ictvdb_id' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case '01.0.2.0.001' '01.0.2.0.002' save_ save__em_virus_entity.entity_assembly_id _item_description.description ; This data item is a pointer to _em_virus_entity.id in the ENTITY_ASSEMBLY category. ; _item.name '_em_virus_entity.entity_assembly_id' _item.category_id em_virus_entity _item.mandatory_code yes _item_type.code code save_ save__em_virus_entity.enveloped _item_description.description ; Flag to indicate if the virus is enveloped or not. ; _item.name '_em_virus_entity.enveloped' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ save__em_virus_entity.empty _item_description.description ; Flag to indicate if the virus is empty or not. ; _item.name '_em_virus_entity.empty' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value YES NO save_ save__em_virus_entity.details _item_description.description ; Additional details about this virus entity ; _item.name '_em_virus_entity.details' _item.category_id em_virus_entity _item.mandatory_code no _item_type.code text save_ ########################## ## EM_ICOS_VIRUS_SHELLS ## ########################## save_em_icos_virus_shells _category.description ; Data items in the EM_ICOS_VIRUS_SHELLS category record details of the viral shell number, diameter of each shell and triangulation number. ; _category.id em_icos_virus_shells _category.mandatory_code no loop_ _category_key.name '_em_icos_virus_shells.virus_entity_id' '_em_icos_virus_shells.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; loop_ _em_icos_virus_shells.virus_entity_id _em_icos_virus_shells.id _em_icos_virus_shells.shell_diameter _em_icos_virus_shells.triangulation_num 1 1 400 4 ; save_ save__em_icos_virus_shells.virus_entity_id _item_description.description ; The value of _em_icos_virus_shells.virus_entity_id is a pointer to _em_virus_entity.id in the VIRUS_ENTITY category. ; _item.name '_em_icos_virus_shells.virus_entity_id' _item.category_id em_icos_virus_shells _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_icos_virus_shells.virus_entity_id' _item_linked.parent_name '_em_virus_entity.id' save_ save__em_icos_virus_shells.id _item_description.description ; The value of _em_em_icos_virus_shells.id must uniquely identify the number and diameter of each virus protein shell and its triangulation number. ; _item.name '_em_icos_virus_shells.id' _item.category_id em_icos_virus_shells _item.mandatory_code yes _item_type.code code save_ save__em_icos_virus_shells.shell_diameter _item_description.description ; The value of the diameter (in angstroms) for each protein shell of the virus. ; _item.name '_em_icos_virus_shells.shell_diameter' _item.category_id em_icos_virus_shells _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_icos_virus_shells.triangulation_num _item_description.description ; The triangulation number (T number) is a geometric and abstract concept that does not correspond to the structural components of an individul virus. It refers to the organisation of the geometric figure. The triangulation number, T is given by the following relationship: T= h*2 + hk +k*2, where h and k are positive integers which define the position of the five-fold vertex on the original hexagonal net. ; _item.name '_em_icos_virus_shells.triangulation_num' _item.category_id em_icos_virus_shells _item.mandatory_code no _item_type.code int _item_examples.case 4 save_ ########################### ## EM_SAMPLE_PREPARATION ## ########################### save_em_sample_preparation _category.description ; Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to loading onto grid support. ; _category.id em_sample_preparation _category.mandatory_code no loop_ _category_key.name '_em_sample_preparation.id' '_em_sample_preparation.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_sample_preparation.entry_id 1DYL _em_sample_preparation.id 1 _em_sample_preparation.ph 7.6 _em_sample_preparation.buffer_id 1 _em_sample_preparation.sample_concentration 5 _em_sample_preparation.2d_crystal_grow_id . _em_sample_preparation.support.id 1 ; save_ save__em_sample_preparation.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_sample_preparation.entry_id' _item.category_id em_sample_preparation _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_sample_preparation.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_sample_preparation.id _item_description.description ; The value of _em_sample_preparation.id must uniquely identify the sample preparation. ; _item.name '_em_sample_preparation.id' _item.category_id em_sample_preparation _item.mandatory_code yes _item_type.code code save_ save__em_sample_preparation.ph _item_description.description ; The pH value of the observed sample buffer. ; _item.name '_em_sample_preparation.ph' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code float save_ save__em_sample_preparation.buffer_id _item_description.description ; This data item is a pointer to _em_buffer.id in the BUFFER category. ; _item.name '_em_sample_preparation.buffer_id' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code code save_ save__em_sample_preparation.sample_concentration _item_description.description ; The value of the concentration (mg/mL for mg per milliliter) of the complex in the sample. ; _item.name '_em_sample_preparation.sample_concentration' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code float _item_units.code mg_per_ml save_ save__em_sample_preparation.2d_crystal_grow_id _item_description.description ; This data item is a pointer to _em_2d_crystal_grow.id in the 2D_CRYSTAL_GROW category. ; _item.name '_em_sample_preparation.2d_crystal_grow_id' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code code save_ save__em_sample_preparation.support_id _item_description.description ; This data item is a pointer to _em_sample_support.id in the EM_SAMPLE_SUPPORT category. ; _item.name '_em_sample_preparation.support_id' _item.category_id em_sample_preparation _item.mandatory_code no _item_type.code code save_ ####################### ## EM_SAMPLE_SUPPORT ## ####################### save_em_sample_support _category.description ; Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied ; _category.id em_sample_support _category.mandatory_code no _category_key.name '_em_sample_support.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_sample_support.id 1 _em_sample_support.film_material 'HOLEY CARBON' _em_sample_support.method . _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 400 _em_sample_support.grid_type MESH _em_sample_support.pretreatment 'GLOW DISCHARGE' _em_sample_support.details . _em_sample_support.citation_id 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_sample_support.id _item_description.description ; The value of _em_sample_support.id must uniquely identify the sample support. ; _item.name '_em_sample_support.id' _item.category_id em_sample_support _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_imaging.sample_support_id' '_em_sample_support.id' '_em_sample_preparation.support_id' '_em_sample_support.id' save_ save__em_sample_support.film_material _item_description.description ; The support material covering the em grid. ; _item.name '_em_sample_support.film_material' _item.category_id em_sample_support _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value CARBON 'FORMVAR PLUS CARBON' 'CELLULOSE ACETATE PLUS CARBON' 'PARLODION PLUS CARBON' 'HOLEY CARBON' save_ save__em_sample_support.method _item_description.description ; A description of the method used to produce the support film. ; _item.name '_em_sample_support.method' _item.category_id em_sample_support _item.mandatory_code no _item_type.code text _item_examples.case '1%formvar in chloroform cast on distilled water' save_ save__em_sample_support.grid_material _item_description.description ; The name of the material from which the grid is made. ; _item.name '_em_sample_support.grid_material' _item.category_id em_sample_support _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value COPPER COPPER/PALLADIUM COPPER/RHODIUM GOLD NICKEL PLATINUM TUNGSTEN TITANIUM MOLYBDENUM save_ save__em_sample_support.grid_mesh_size _item_description.description ; The value of the mesh size (per inch) of the em grid. ; _item.name '_em_sample_support.grid_mesh_size' _item.category_id em_sample_support _item.mandatory_code no _item_type.code int _item_examples.case 400 save_ save__em_sample_support.grid_type _item_description.description ; A description of the grid type. ; _item.name '_em_sample_support.grid_type' _item.category_id em_sample_support _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value SLOT APERTURE DIAMOND HEXAGONAL save_ save__em_sample_support.pretreatment _item_description.description ; A description of the grid plus support film pretreatment. ; _item.name '_em_sample_support.pretreatment' _item.category_id em_sample_support _item.mandatory_code no _item_type.code text _item_examples.case 'glow-discharged for 30 sec in argon' save_ save__em_sample_support.details _item_description.description ; A description of any additional details concerning the sample support. ; _item.name '_em_sample_support.details' _item.category_id em_sample_support _item.mandatory_code no _item_type.code text _item_examples.case 'This grid plus sample was kept at -170 deg C for a month before use' save_ save__em_sample_support.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_sample_support.citation_id' _item.category_id em_sample_support _item.mandatory_code no _item_linked.child_name '_em_sample_support.citation_id' _item_linked.parent_name '_citation.id' _item_type.code code save_ ########################## ## EM_2D_CRYSTAL_GROW ## ########################## save_em_2d_crystal_grow _category.description ; Data items in the EM_2D_CRYSTAL_GROW category record details of growth conditions for 2d crystal samples. ; _category.id em_2d_crystal_grow _category.mandatory_code no _category_key.name '_em_2d_crystal_grow.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1AT9 and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_2d_crystal_grow.id 1 _em_2d_crystal_grow.method . _em_2d_crystal_grow.apparatus . _em_2d_crystal_grow.atmosphere 'room air' _em_2d_crystal_grow.pH 5.2 _em_2d_crystal_grow.temp 18 _em_2d_crystal_grow.time . _em_2d_crystal_grow.buffer_id 2 _em_2d_crystal_grow.details 'on grid' _em_2d_crystal_grow.number_2d_crystals 129 _em_2d_crystal_grow.mean_2d_crystal_size . _em_2d_crystal_grow.citation_id 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__em_2d_crystal_grow.id _item_description.description ; The value of _em_2d_crystal_grow.crystal_id must uniquely identify the sample 2d crystal. ; _item.name '_em_2d_crystal_grow.id' _item.category_id em_2d_crystal_grow _item.mandatory_code yes _item_type.code code save_ save__em_2d_crystal_grow.method _item_description.description ; The method used for growing the crystals. ; _item.name '_em_2d_crystal_grow.method' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'lipid monolayer' save_ save__em_2d_crystal_grow.apparatus _item_description.description ; The type of the apparatus used for growing the crystals. ; _item.name '_em_2d_crystal_grow.apparatus' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'Langmuir trough' save_ save__em_2d_crystal_grow.atmosphere _item_description.description ; The type of atmosphere in which crystals were grown. ; _item.name '_em_2d_crystal_grow.atmosphere' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'room air' save_ save__em_2d_crystal_grow.pH _item_description.description ; the pH value used for growing the crystals. ; _item.name '_em_2d_crystal_grow.pH' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code float _item_examples.case 4.7 save_ save__em_2d_crystal_grow.temp _item_description.description ; The value of the temperature in degrees Kelvin used for growing the crystals. ; _item.name '_em_2d_crystal_grow.temp' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_examples.case 293 save_ save__em_2d_crystal_grow.time _item_description.description ; The length of time required to grow the crystals. ; _item.name '_em_2d_crystal_grow.time' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code line _item_examples.case 'approximately 2 days' save_ save__em_2d_crystal_grow.buffer_id _item_description.description ; This data item is a pointer to _em_buffer.id in the BUFFER category. ; _item.name '_em_2d_crystal_grow.buffer_id' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code code save_ save__em_2d_crystal_grow.details _item_description.description ; Any additional items concerning 2d crystal growth. ; _item.name '_em_2d_crystal_grow.details' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code text save_ save__em_2d_crystal_grow.number_2d_crystals _item_description.description ; The number of 2d crystals imaged. ; _item.name '_em_2d_crystal_grow.number_2d_crystals' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code int save_ save__em_2d_crystal_grow.mean_2d_crystal_size _item_description.description ; The approximate size (microns squared) of 2d crystals imaged. ; _item.name '_em_2d_crystal_grow.mean_2d_crystal_size' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_type.code float _item_units.code microns_squared save_ save__em_2d_crystal_grow.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_2d_crystal_grow.citation_id' _item.category_id em_2d_crystal_grow _item.mandatory_code no _item_linked.child_name '_em_2d_crystal_grow.citation_id' _item_linked.parent_name '_citation.id' _item_type.code code save_ ############### ## EM_BUFFER ## ############### save_em_buffer _category.description ; Data items in the BUFFER category record details of the sample buffer. ; _category.id em_buffer _category.mandatory_code no _category_key.name '_em_buffer.id' loop_ _category_group.id 'inclusive_group' 'em_group' save_ save__em_buffer.id _item_description.description ; The value of _em_buffer.id must uniquely identify the sample buffer. ; _item.name '_em_buffer.id' _item.category_id em_buffer _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_2d_crystal_grow.buffer_id' '_em_buffer.id' '_em_sample_preparation.buffer_id' '_em_buffer.id' '_em_buffer_components.buffer_id' '_em_buffer.id' save_ save__em_buffer.name _item_description.description ; The name of the buffer. ; _item.name '_em_buffer.name' _item.category_id em_buffer _item.mandatory_code no _item_type.code line _item_examples.case 'Acetic acid' save_ save__em_buffer.details _item_description.description ; Any additional details to do with buffer. ; _item.name '_em_buffer.details' _item.category_id em_buffer _item.mandatory_code no _item_type.code text _item_examples.case 'aerated' save_ ########################## ## EM_BUFFER_COMPONENTS ## ########################## save_em_buffer_components _category.description ; Constituents of buffer in sample ; _category.id em_buffer_components _category.mandatory_code no loop_ _category_key.name '_em_buffer_components.buffer_id' '_em_buffer_components.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ;loop_ _em_buffer_components.buffer_id _em_buffer_components.id _em_buffer_components.name _em_buffer_components.volume _em_buffer_components.conc _em_buffer_components.details 1 1 'NaCl' '0.200 ' '4 ' . 1 2 'Acetic Acid' '0.047 ' '100' . 1 3 'water' '0.700 ' 'neat' . ; save_ save__em_buffer_components.id _item_description.description ; The value of _em_buffer_components.id must uniquely identify a component of the buffer. ; _item.name '_em_buffer_components.id' _item.category_id em_buffer_components _item.mandatory_code yes _item_type.code code save_ save__em_buffer_components.buffer_id _item_description.description ; This data item is a pointer to _em_buffer.id in the BUFFER category. ; _item.name '_em_buffer_components.buffer_id' _item.category_id em_buffer_components _item.mandatory_code yes _item_type.code code save_ save__em_buffer_components.name _item_description.description ; The name of each buffer component. ; _item.name '_em_buffer_components.name' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code line _item_examples.case 'Acetic acid' save_ save__em_buffer_components.volume _item_description.description ; The volume of buffer component. ; _item.name '_em_buffer_components.volume' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code code _item_examples.case 0.200 save_ save__em_buffer_components.conc _item_description.description ; The millimolar concentration of buffer component. ; _item.name '_em_buffer_components.conc' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code code _item_examples.case 200 save_ save__em_buffer_components.details _item_description.description ; Any additional details to do with buffer composition. ; _item.name '_em_buffer_components.details' _item.category_id em_buffer_components _item.mandatory_code no _item_type.code text _item_examples.case 'pH adjusted with NaOH' save_ ###################### ## EM_VITRIFICATION ## ###################### save_em_vitrification _category.description ; Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope ; _category.id em_vitrification _category.mandatory_code no loop_ _category_key.name '_em_vitrification.id' '_em_vitrification.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_vitrification.entry_id 1DYL _em_vitrification.id 1 _em_vitrification.sample_preparation_id 1 _em_vitrification.cryogen_name "ETHANE" _em_vitrification.humidity 90 _em_vitrification.temp 95 _em_vitrification.instrument . _em_vitrification.method "PLUNGE VITRIFICATION" _em_vitrification.time_resolved_state . _em_vitrification.citation_id 1 _em_vitrification.details ; SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER. ; ; save_ save__em_vitrification.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_vitrification.entry_id' _item.category_id em_vitrification _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_vitrification.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_vitrification.id _item_description.description ; The value of _em_vitrification.id must uniquely identify the vitrification procedure. ; _item.name '_em_vitrification.id' _item.category_id em_vitrification _item.mandatory_code yes _item_type.code code save_ save__em_vitrification.sample_preparation_id _item_description.description ; This data item is a pointer to _em_sample_preparation.id in the EM_SAMPLE_PREPARATION category. ; _item.name '_em_vitrification.sample_preparation_id' _item.category_id em_vitrification _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_vitrification.sample_preparation_id' _item_linked.parent_name '_em_sample_preparation.id' save_ save__em_vitrification.cryogen_name _item_description.description ; This is the name of the cryogen. ; _item.name '_em_vitrification.cryogen_name' _item.category_id em_vitrification _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value HELIUM NITROGEN PROPANE ETHANE METHANE 'FREON 22' 'FREON 12' save_ save__em_vitrification.humidity _item_description.description ; The humidity (%) in the vicinity of the vitrification process. ; _item.name '_em_vitrification.humidity' _item.category_id em_vitrification _item.mandatory_code no _item_type.code line _item_examples.case 90 save_ save__em_vitrification.temp _item_description.description ; The temperature (in degrees Kelvin) at which vitrification took place. ; _item.name '_em_vitrification.temp' _item.category_id em_vitrification _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_examples.case 4.2 save_ save__em_vitrification.instrument _item_description.description ; The type of instrument used in the vitrification process. ; _item.name '_em_vitrification.instrument' _item.category_id em_vitrification _item.mandatory_code no _item_type.code line _item_examples.case 'Reichert plunger' save_ save__em_vitrification.method _item_description.description ; The procedure for vitrification. ; _item.name '_em_vitrification.method' _item.category_id em_vitrification _item.mandatory_code no _item_type.code text _item_examples.case 'blot for 2 seconds before plunging' save_ save__em_vitrification.time_resolved_state _item_description.description ; The length of time after an event effecting the sample that vitrification was induced and a description of the event. ; _item.name '_em_vitrification.time_resolved_state' _item.category_id em_vitrification _item.mandatory_code no _item_type.code text _item_examples.case '30 msec after spraying with effector'' save_ save__em_vitrification.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_vitrification.citation_id' _item.category_id em_vitrification _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_vitrification.citation_id' _item_linked.parent_name '_citation.id' save_ save__em_vitrification.details _item_description.description ; Any additional details relating to vitrification. ; _item.name '_em_vitrification.details' _item.category_id em_vitrification _item.mandatory_code no _item_type.code text _item_examples.case 'argon atmosphere' save_ ################ ## EM_IMAGING ## ################ save_em_imaging _category.description ; Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope. ; _category.id em_imaging _category.mandatory_code no loop_ _category_key.name '_em_imaging.entry_id' '_em_imaging.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_imaging.entry_id 1DYL _em_imaging.id 1 _em_imaging.sample_support_id 1 _em_imaging.microscope_model 'FEI/PHILIPS CM200 FEG' _em_imaging.specimen_holder_type 'cryotransfer' _em_imaging.specimen_holder_model 'gatan 626-0300' _em_imaging.details . _em_imaging.date 1998-15-06 _em_imaging.accelerating_voltage 200 _em_imaging.illumination_mode 'bright field' _em_imaging.mode 'low dose' _em_imaging.nominal_cs 2.0 _em_imaging.nominal_defocus_min 975 _em_imaging.nominal_defocus_max 7600 _em_imaging.tilt_angle_min 0 _em_imaging.tilt_angle_max 0 _em_imaging.nominal_magnification 50000 _em_imaging.calibrated_magnification . _em_imaging.electron_source 'FEG' _em_imaging.electron_dose . _em_imaging.energy_filter . _em_imaging.energy_window . _em_imaging.citation_id 1 _em_imaging.temperature 95 _em_imaging.detector_distance . _em_imaging.recording_temp_range . ; save_ save__em_imaging.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_imaging.entry_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_imaging.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_imaging.id _item_description.description ; The value of _em_imaging.id must uniquely identify each imaging experiment. ; _item.name '_em_imaging.id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.sample_support_id _item_description.description ; This data item is a pointer to _em_sample_support.id in the EM_SAMPLE_SUPPORT category. ; _item.name '_em_imaging.sample_support_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.detector_id _item_description.description ; The value of _em_imaging.detector_id must uniquely identify the type of detector used in the experiment. ; _item.name '_em_imaging.detector_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.scans_id _item_description.description ; The value of _em_imaging.scans_id must uniquely identify the image_scans used in the experiment. ; _item.name '_em_imaging.scans_id' _item.category_id em_imaging _item.mandatory_code yes _item_type.code code save_ save__em_imaging.microscope_model _item_description.description ; The name of the model of microscope. ; _item.name '_em_imaging.microscope_model' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'HITACHI H8100' 'HITACHI HF2000' 'HITACHI HF2000-UHR' 'HITACHI H9000-UHR' 'HITACHI H9000-NAR' 'HITACHI 300KEV FEG' 'HITACHI HU1250' 'HITACHI H-1500' 'JEOL 2000EX' 'JEOL 2010HT' 'JEOL 2010UHR' 'JEOL 2010F' 'JEOL 3010HT' 'JEOL 3010UHR' 'JEOL KYOTO-3000SFF' 'JEOL 4000EX' 'JEOL HAREM' 'JEOL ARM-1000' 'JEOL KYOTO-1000' 'JEOL ARM-1250' 'FEI/PHILIPS CM120T' 'FEI/PHILIPS CM200T' 'FEI/PHILIPS CM20/ST' 'FEI/PHILIPS CM20/SOPHIE' 'FEI/PHILIPS CM200FEG/ST' 'FEI/PHILIPS CM20/UT' 'FEI/PHILIPS CM200FEG/UT' 'FEI/PHILIPS CM30/T' 'FEI/PHILIPS CM300FEG/T' 'FEI/PHILIPS CM300FEG/HE' 'FEI/PHILIPS CM30/ST' 'FEI/PHILIPS CM300FEG/ST' 'FEI/PHILIPS CM300FEG/UT' 'FEI TECNAI 12' 'FEI TECNAI 20' 'FEI TECNAI F20' 'FEI TECNAI F30' 'FEI MORGAGNI' save_ save__em_imaging.specimen_holder_type _item_description.description ; The type of specimen holder used during imaging. ; _item.name '_em_imaging.specimen_holder_type' _item.category_id em_imaging _item.mandatory_code no _item_type.code line _item_examples.case 'cryo' save_ save__em_imaging.specimen_holder_model _item_description.description ; The name of the model of specimen holder used during imaging. ; _item.name '_em_imaging.specimen_holder_model' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'GATAN HELIUM' 'GATAN LIQUID NITROGEN' OTHER save_ save__em_imaging.details _item_description.description ; Any additional imaging details. ; _item.name '_em_imaging.details' _item.category_id em_imaging _item.mandatory_code no _item_type.code text _item_examples.case 'weak beam illumination' save_ save__em_imaging.date _item_description.description ; Date (YYYY-MM-DD) of imaging experiment or the date at which a series of experiments began. ; _item.name '_em_imaging.date' _item.category_id em_imaging _item.mandatory_code no # _item_type.code yyyy-mm-dd _item_type.code line _item_examples.case '2001-05-08' save_ save__em_imaging.accelerating_voltage _item_description.description ; A value of accelerating voltage (in kV) used for imaging. ; _item.name '_em_imaging.accelerating_voltage' _item.category_id em_imaging _item.mandatory_code no _item_type.code int _item_units.code kilovolts _item_examples.case 300 save_ save__em_imaging.illumination_mode _item_description.description ; The mode of illumination. ; _item.name '_em_imaging.illumination_mode' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'FLOOD BEAM' 'FLOOD BEAM LOW DOSE' 'SPOT SCAN' OTHER save_ save__em_imaging.mode _item_description.description ; The mode of imaging. ; _item.name '_em_imaging.mode' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'BRIGHT FIELD' 'DARK FIELD' DIFFRACTION OTHER save_ save__em_imaging.nominal_cs _item_description.description ; The spherical aberration coefficient (Cs) in millimetres, of the objective lens. ; _item.name '_em_imaging.nominal_cs' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code millimetres _item_examples.case 1.4 save_ save__em_imaging.nominal_defocus_min _item_description.description ; The minimum defocus value of the objective lens (in nanometres) used to obtain the recorded images. ; _item.name '_em_imaging.nominal_defocus_min' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_examples.case 975 save_ save__em_imaging.nominal_defocus_max _item_description.description ; The maximum defocus value of the objective lens (in nanometres) used to obtain the recorded images. ; _item.name '_em_imaging.nominal_defocus_max' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_examples.case 7600 save_ save__em_imaging.tilt_angle_min _item_description.description ; The minimum angle at which the specimen was tilted to obtain recorded images. ; _item.name '_em_imaging.tilt_angle_min' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 0 save_ save__em_imaging.tilt_angle_max _item_description.description ; The maximum angle at which the specimen was tilted to obtain recorded images. ; _item.name '_em_imaging.tilt_angle_max' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 60 save_ save__em_imaging.nominal_magnification _item_description.description ; The magnification indicated by the microscope readout. ; _item.name '_em_imaging.nominal_magnification' _item.category_id em_imaging _item.mandatory_code no _item_type.code int _item_examples.case 60000 save_ save__em_imaging.calibrated_magnification _item_description.description ; The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. ; _item.name '_em_imaging.calibrated_magnification' _item.category_id em_imaging _item.mandatory_code no _item_type.code int _item_examples.case 61200 save_ save__em_imaging.electron_source _item_description.description ; The source of electrons. The electron gun. ; _item.name '_em_imaging.electron_source' _item.category_id em_imaging _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'FIELD EMISSION GUN' LAB6 'TUNGSTEN HAIRPIN' 'SCHOTTKY FIELD EMISSION GUN' OTHER save_ save__em_imaging.electron_dose _item_description.description ; The electron dose received by the specimen (electrons per square angstrom). ; _item.name '_em_imaging.electron_dose' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code electrons_angstrom_squared _item_examples.case 0.9 save_ save__em_imaging.energy_filter _item_description.description ; The type of energy filter spectrometer apparatus. ; _item.name '_em_imaging.energy_filter' _item.category_id em_imaging _item.mandatory_code no _item_type.code line _item_examples.case 'FEI' save_ save__em_imaging.energy_window _item_description.description ; The energy filter range in electron volts (eV)set by spectrometer. ; _item.name '_em_imaging.energy_window' _item.category_id em_imaging _item.mandatory_code no _item_type.code line _item_units.code electron_volts _item_examples.case '0 - 15' save_ save__em_imaging.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_imaging.citation_id' _item.category_id em_imaging _item.mandatory_code no _item_linked.child_name '_em_imaging.citation_id' _item_linked.parent_name '_citation.id' _item_type.code code save_ save__em_imaging.temperature _item_description.description ; The mean specimen stage temperature (degrees Kelvin) during imaging in the microscope. ; _item.name '_em_imaging.temperature' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ save__em_imaging.detector_distance _item_description.description ; The camera length (in millimetres). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. ; _item.name '_em_imaging.detector_distance' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code millimetres save_ save__em_imaging.recording_temperature_minimum _item_description.description ; The specimen temperature minimum (degrees Kelvin) for the duration of imaging. ; _item.name '_em_imaging.recording_temperature_minimum' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ save__em_imaging.recording_temperature_maximum _item_description.description ; The specimen temperature maximum (degrees Kelvin) for the duration of imaging. ; _item.name '_em_imaging.recording_temperature_maximum' _item.category_id em_imaging _item.mandatory_code no _item_type.code float _item_units.code kelvins save_ ################# ## EM_DETECTOR ## ################# save_em_detector _category.description ; Data items in the EM_DETECTOR category record details of the image detector type. ; _category.id em_detector _category.mandatory_code no loop_ _category_key.name '_em_detector.entry_id' '_em_detector.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_detector.entry_id 1DYL _em_detector.id 1 _em_detector.details . _em_detector.type 'KODAK SO163 FILM' _em_detector.detective_quantum_efficiency . ; save_ save__em_detector.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_detector.entry_id' _item.category_id em_detector _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_detector.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_detector.id _item_description.description ; The value of _em_detector.id must uniquely identify the detector used for imaging. ; _item.name '_em_detector.id' _item.category_id em_detector _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_imaging.detector_id' '_em_detector.id' save_ save__em_detector.details _item_description.description ; Any additional information about the detection system. ; _item.name '_em_detector.details' _item.category_id em_detector _item.mandatory_code no _item_type.code text save_ save__em_detector.type _item_description.description ; The detector type used for recording images. Usually film or CCD camera. ; _item.name '_em_detector.type' _item.category_id em_detector _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'KODAK SO163 FILM' 'GATAN 673' 'GATAN 676' 'GATAN 692' 'GATAN 794' 'GATAN 1000' 'GATAN 4000' 'TVIPS BIOCAM' 'TVIPS TEMCAM F214' 'TVIPS TEMCAM F224' 'TVIPS FASTSCAN F114' PROSCAN AMT save_ save__em_detector.detective_quantum_efficiency _item_description.description ; The detective_quantum_efficiency (DQE)is defined as the square of the signal-to-noise ratio in the recording device divided by the square of the signal-to-ratio in the electron beam: (SIGNAL/NOISE)2 recording device DQE = ------------------------------- (SIGNAL/NOISE)2 electron beam A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas that the signal-to-noise ratio is reduced by half in the recording step. (0.5)**2 DQE = --------- = 0.25. (1.0)**2 ; _item.name '_em_detector.detective_quantum_efficiency' _item.category_id em_detector _item.mandatory_code no _item_type.code float _item_examples.case 0.25 save_ #################### ## EM_IMAGE_SCANS ## #################### save_em_image_scans _category.description ; Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image. ; _category.id em_image_scans _category.mandatory_code no loop_ _category_key.name '_em_image_scans.entry_id' '_em_image_scans.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_image_scans.entry_id 1DYL _em_image_scans.id 2 _em_image_scans.number_digital_images 48 _em_image_scans.details . _em_image_scans.scanner_model . _em_image_scans.sampling_size . _em_image_scans.od_range . _em_image_scans.quant_bit_number . _em_image_scans.citation_id 1 ; save_ save__em_image_scans.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_image_scans.entry_id' _item.category_id em_image_scans _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_image_scans.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_image_scans.id _item_description.description ; The value of _em_image_scans.id must uniquely identify the images scanned. ; _item.name '_em_image_scans.id' _item.category_id em_image_scans _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_em_imaging.scans_id' '_em_image_scans.id' save_ save__em_image_scans.number_digital_images _item_description.description ; The number of images scanned and digitised. ; _item.name '_em_image_scans.number_digital_images' _item.category_id em_image_scans _item.mandatory_code no _item_type.code int save_ save__em_image_scans.details _item_description.description ; Any additional details about scanning images. ; _item.name '_em_image_scans.details' _item.category_id em_image_scans _item.mandatory_code no _item_type.code text save_ save__em_image_scans.scanner_model _item_description.description ; The scanner model. ; _item.name '_em_image_scans.scanner_model' _item.category_id em_image_scans _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value 'ZEISS SCAI' 'EMIL 10' OPTRONICS 'PERKIN ELMER' TEMSCAN OTHER save_ save__em_image_scans.sampling_size _item_description.description ; The sampling step size (microns) set on the scanner. ; _item.name '_em_image_scans.sampling_size' _item.category_id em_image_scans _item.mandatory_code no _item_type.code float _item_units.code microns save_ save__em_image_scans.od_range _item_description.description ; The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light grey and OD=3 is opaque. ; _item.name '_em_image_scans.od_range' _item.category_id em_image_scans _item.mandatory_code no _item_type.code float _item_examples.case 1.4 save_ save__em_image_scans.quant_bit_size _item_description.description ; The number of bits per pixel. ; _item.name '_em_image_scans.quant_bit_size' _item.category_id em_image_scans _item.mandatory_code no _item_type.code int _item_examples.case 8 save_ save__em_image_scans.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_image_scans.citation_id' _item.category_id em_image_scans _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_image_scans.citation_id' _item_linked.parent_name '_citation.id' save_ ################################ ## EM_2D_PROJECTION_SELECTION ## ################################ save_em_2d_projection_selection _category.description ; Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. ; _category.id em_2d_projection_selection _category.mandatory_code no _category_key.name '_em_2d_projection_selection.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_2d_projection_selection.entry_id 1 _em_2d_projection_selection.number_particles 5267 _em_2d_projection_selection.software_name 1 _em_2d_projection_selection.method 'INTERACTIVE' _em_2d_projection_selection.details . _em_2d_projection_selection.citation_id 1 ; save_ save__em_2d_projection_selection.entry_id _item_description.description ; The value of _em_2d_projection_selection.entry_id points to the ENTRY category. ; _item.name '_em_2d_projection_selection.entry_id' _item.category_id em_2d_projection_selection _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_2d_projection_selection.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_2d_projection_selection.num_particles _item_description.description ; The number of particles selected from the projection set of images. ; _item.name '_em_2d_projection_selection.num_particles' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code int _item_examples.case 840 save_ save__em_2d_projection_selection.software_name _item_description.description ; This data item is a pointer to _software.name in the SOFTWARE category. ; _item.name '_em_2d_projection_selection.software_name' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code line # _item_linked.child_name '_em_2d_projection_selection.software_name' # _item_linked.parent_name '_software.name' save_ save__em_2d_projection_selection.method _item_description.description ; The method used for selecting observed assemblies. ; _item.name '_em_2d_projection_selection.method' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code text _item_examples.case 'particles picked interactively from monitor' save_ save__em_2d_projection_selection.details _item_description.description ; Any additional details used for selecting observed assemblies. ; _item.name '_em_2d_projection_selection.details' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code text _item_examples.case 'negative monitor contrast facilitated particle picking' save_ save__em_2d_projection_selection.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_2d_projection_selection.citation_id' _item.category_id em_2d_projection_selection _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_2d_projection_selection.citation_id' _item_linked.parent_name '_citation.id' save_ ################################# ## EM_EULER_ANGLE_DISTRIBUTION ## ################################# save_em_euler_angle_distribution _category.description ; Data items in the EM_EULER_ANGLE_DISTRIBUTION category record details of assignment of Euler angles for projection sets of particles. ; _category.id em_euler_angle_distribution _category.mandatory_code no loop_ _category_key.name '_em_euler_angle_distribution.id' '_em_euler_angle_distribution.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_euler_angle_distribution.entry_id 1DYL _em_euler_angle_distribution.id 1 _em_euler_angle_distribution.details . _em_euler_angle_distribution.alpha . _em_euler_angle_distribution.beta . _em_euler_angle_distribution.gamma . ; save_ save__em_euler_angle_distribution.id _item_description.description ; The value of _em_euler_angle_distribution.id must uniquely identify the euler angle assignments of the projection set used in the final reconstruction. ; _item.name '_em_euler_angle_distribution.id' _item.category_id em_euler_angle_distribution _item.mandatory_code yes _item_type.code code save_ save__em_euler_angle_distribution.entry_id _item_description.description ; The value of _em_euler_angle_distribution.entry_id is a pointer to the ENTRY category. ; _item.name '_em_euler_angle_distribution.entry_id' _item.category_id em_euler_angle_distribution _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_euler_angle_distribution.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_euler_angle_distribution.details _item_description.description ; Any additional details of the euler angles distribution and assignment. ; _item.name '_em_euler_angle_distribution.details' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code text save_ save__em_euler_angle_distribution.alpha _item_description.description ; The euler-alpha angle assignment. ; _item.name '_em_euler_angle_distribution.alpha' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 90 save_ save__em_euler_angle_distribution.beta _item_description.description ; The euler-beta angle assignment. ; _item.name '_em_euler_angle_distribution.beta' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 90 save_ save__em_euler_angle_distribution.gamma _item_description.description ; The euler-gamma angle assignment. ; _item.name '_em_euler_angle_distribution.gamma' _item.category_id em_euler_angle_distribution _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 0 save_ ########################## ## EM_3D_RECONSTRUCTION ## ########################## save_em_3d_reconstruction _category.description ; Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. ; _category.id em_3d_reconstruction _category.mandatory_code no loop_ _category_key.name '_em_3d_reconstruction.entry_id' '_em_3d_reconstruction.id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_reconstruction.entry_id 1DYL _em_3d_reconstruction.id 1 _em_3d_reconstruction.method 'CROSS-COMMON LINES' _em_3d_reconstruction.citation_id 1 _em_3d_reconstruction.details . _em_3d_reconstruction.resolution 9 _em_3d_reconstruction.resolution_method . _em_3d_reconstruction.ctf_correction_method . _em_3d_reconstruction.nominal_pixel_size 2.64 _em_3d_reconstruction.actual_pixel_size 2.52 ; save_ save__em_3d_reconstruction.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_3d_reconstruction.entry_id' _item.category_id em_3d_reconstruction _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_3d_reconstruction.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_reconstruction.id _item_description.description ; The value of _em_3d_reconstruction.id must uniquely identify the 3d reconstruction. ; _item.name '_em_3d_reconstruction.id' _item.category_id em_3d_reconstruction _item.mandatory_code yes _item_type.code code save_ save__em_3d_reconstruction.method _item_description.description ; The algorithm method used for the 3d-reconstruction. ; _item.name '_em_3d_reconstruction.method' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'cross-common lines' save_ save__em_3d_reconstruction.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_em_3d_reconstruction.citation_id' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code code _item_linked.child_name '_em_3d_reconstruction.citation_id' _item_linked.parent_name '_citation.id' save_ save__em_3d_reconstruction.details _item_description.description ; Any additional details used in the 3d reconstruction. ; _item.name '_em_3d_reconstruction.details' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.resolution _item_description.description ; The final resolution (in angstroms)of the 3d reconstruction. ; _item.name '_em_3d_reconstruction.resolution' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__em_3d_reconstruction.resolution_method _item_description.description ; The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. ; _item.name '_em_3d_reconstruction.resolution_method' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'FSC at 0.5 cut-off' save_ save__em_3d_reconstruction.magnification_calibration _item_description.description ; The magnification calibration method for the 3d reconstruction. ; _item.name '_em_3d_reconstruction.magnification_calibration' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text save_ save__em_3d_reconstruction.ctf_correction_method _item_description.description ; The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. ; _item.name '_em_3d_reconstruction.ctf_correction_method' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code text _item_examples.case 'CTF correction of each particle' save_ save__em_3d_reconstruction.nominal_pixel_size _item_description.description ; The nominal pixel size of the projection set of images. ; _item.name '_em_3d_reconstruction.nominal_pixel_size' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ save__em_3d_reconstruction.actual_pixel_size _item_description.description ; The actual pixel size of projection set of images. ; _item.name '_em_3d_reconstruction.actual_pixel_size' _item.category_id em_3d_reconstruction _item.mandatory_code no _item_type.code float save_ ################### ## EM_3D_FITTING ## ################### save_em_3d_fitting _category.description ; Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file ; _category.id em_3d_fitting _category.mandatory_code no loop_ _category_key.name '_em_3d_fitting.id' '_em_3d_fitting.entry_id' loop_ _category_group.id 'em_group' 'inclusive_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_fitting.id 1 _em_3d_fitting.entry_id 1DYL _em_3d_fitting.method AUTOMATIC _em_3d_fitting.target_criteria R-FACTOR _em_3d_fitting.software_name 1 _em_3d_fitting.over_all_b_value . _em_3d_fitting.ref_space REAL _em_3d_fitting.ref_protocol 'RIGID BODY REFINEMENT' _em_3d_fitting.details ; THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. ; ; save_ save__em_3d_fitting.id _item_description.description ; The value of _em_3d_fitting.id must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map. ; loop_ _item.name _item.category_id _item.mandatory_code '_em_3d_fitting.id' em_3d_fitting yes '_em_3d_fitting_list.3d_fitting_id' em_3d_fitting_list yes loop_ _item_linked.child_name _item_linked.parent_name '_em_3d_fitting_list.3d_fitting_id' '_em_3d_fitting.id' _item_type.code code save_ save__em_3d_fitting.entry_id _item_description.description ; This data item is a pointer to _entry_id in the ENTRY category. ; _item.name '_em_3d_fitting.entry_id' _item.category_id em_3d_fitting _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_3d_fitting.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_3d_fitting.method _item_description.description ; The method used to fit atomic coordinates into the 3dem reconstructed map. ; _item.name '_em_3d_fitting.method' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line save_ save__em_3d_fitting.target_criteria _item_description.description ; The quality of fit of the atomic coordinates into the 3dem volume map. ; _item.name '_em_3d_fitting.target_criteria' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'best visual fit using the program O' save_ save__em_3d_fitting.software_name _item_description.description ; This data item is a pointer to _software.name in the category. ; _item.name '_em_3d_fitting.software_name' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line # _item_linked.child_name '_em_3d_fitting.software_name' # _item_linked.parent_name '_software.name' save_ save__em_3d_fitting.details _item_description.description ; Any additional details regarding fitting of atomic coordinates into the 3d-em volume. ; _item.name '_em_3d_fitting.details' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'partial' save_ save__em_3d_fitting.overall_b_value _item_description.description ; The overall B (temperature factor) value for the 3d-em volume. ; _item.name '_em_3d_fitting.overall_b_value' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code float save_ save__em_3d_fitting.ref_space _item_description.description ; A flag to indicate whether fitting was carried out in real or reciprocal refinement space. ; _item.name '_em_3d_fitting.ref_space' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value REAL RECIPROCAL save_ save__em_3d_fitting.ref_protocol _item_description.description ; The type of protocol used in the refinement. ; _item.name '_em_3d_fitting.ref_protocol' _item.category_id em_3d_fitting _item.mandatory_code no _item_type.code text _item_examples.case 'rigid body' save_ ######################## ## EM_3D_FITTING_LIST ## ######################## save_em_3d_fitting_list _category.description ; Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file ; _category.id em_3d_fitting_list _category.mandatory_code no loop_ _category_key.name '_em_3d_fitting_list.id' '_em_3d_fitting_list.3d_fitting_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL ; ; _em_3d_fitting_list.id 1 _em_3d_fitting_list.fitting_id l _em_3d_fitting_list.pdb_entry_id 1VCQ _em_3d_fitting_list.pdb_chain_id . ; save_ save__em_3d_fitting_list.id _item_description.description ; This data item is a unique identifier. ; _item.name '_em_3d_fitting_list.id' _item.category_id em_3d_fitting_list _item.mandatory_code yes _item_type.code code save_ save__em_3d_fitting_list.3d_fitting_id _item_description.description ; The value of _em_3d_fitting_list.3d_fitting_id is a pointer to _em_3d_fitting.id in the 3d_fitting category ; _item.name '_em_3d_fitting_list.3d_fitting_id' _item.mandatory_code yes save_ save__em_3d_fitting_list.pdb_entry_id _item_description.description ; The PDB code for the entry used in fitting. ; _item.name '_em_3d_fitting_list.pdb_entry_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code line save_ save__em_3d_fitting_list.pdb_chain_id _item_description.description ; The chain id for the entry used in fitting. ; _item.name '_em_3d_fitting_list.pdb_chain_id' _item.category_id em_3d_fitting_list _item.mandatory_code no _item_type.code code save_ ############################# ## EM_ELECTRON_DIFFRACTION ## ############################# save_em_electron_diffraction _category.description ; Data items in the EM_ELECTRON_DIFFRACTION category record details about the electron diffraction data from the electron crystallography experiment. ; _category.id em_electron_diffraction _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction.id' '_em_electron_diffraction.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1TUB and laboratory records for the structure corresponding to PDB entry 1TUB ; ; _em_electron_diffraction.entry_id 1TUB _em_electron_diffraction.id 1 _em_electron_diffraction.num_structure_factors 12000 _em_electron_diffraction.num_diff_patterns . _em_electron_diffraction.details . ; save_ save__em_electron_diffraction.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_em_electron_diffraction.entry_id' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_electron_diffraction.id _item_description.description ; The value of _electron_diffraction.id must uniquely identify the electron diffraction experiment. ; _item.name '_em_electron_diffraction.id' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction.num_structure_factors _item_description.description ; The number of structure factors from the electron diffraction experiment. ; _item.name '_em_electron_diffraction.num_structure_factors' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int _item_examples.case '12000' save_ save__em_electron_diffraction.num_diff_patterns _item_description.description ; The number of diffraction patterns used from the electron diffraction experiment. ; _item.name '_em_electron_diffraction.num_diff_patterns' _item.category_id em_electron_diffraction _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction.details _item_description.description ; Details of the electron diffraction experiment ; _item.name '_em_electron_diffraction.details' _item.category_id em_electron_diffraction _item.mandatory_code yes _item_type.code text loop_ _item_examples.case _item_examples.detail 1 ; THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE. ; save_ ################################### ## EM_ELECTRON_DIFFRACTION_PHASE ## ################################### save_em_electron_diffraction_phase _category.description ; data items in the em_electron_diffraction_phase category record details about the phase information from the electron diffraction experiment. ; _category.id em_electron_diffraction_phase _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction_phase.id' '_em_electron_diffraction_phase.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub ; ; _em_electron_diffraction_phase.entry_id 1TUB _em_electron_diffraction_phase.id 1 _em_electron_diffraction_phase.d_res_low 5.0 _em_electron_diffraction_phase.d_res_high 4.0 _em_electron_diffraction_phase.residual . _em_electron_diffraction_phase.highest_resolution_shell_error . _em_electron_diffraction_phase.overall_error . _em_electron_diffraction_phase.rejection_criteria_error . ; save_ save__em_electron_diffraction_phase.entry_id _item_description.description ; this data item is a pointer to _entry.id in the entry category. ; _item.name '_em_electron_diffraction_phase.entry_id' _item.category_id em_electron_diffraction_phase _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction_phase.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_electron_diffraction_phase.id _item_description.description ; the value of _electron_diffraction_phase.id must uniquely identify the electron diffraction phase experiment. ; _item.name '_em_electron_diffraction_phase.id' _item.category_id em_electron_diffraction_phase _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction_phase.d_res_high _item_description.description ; the highest resolution d-value for the electron diffraction experiment. ; _item.name '_em_electron_diffraction_phase.d_res_high' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int _item_examples.case '5.0' save_ save__em_electron_diffraction_phase.residual _item_description.description ; the phase residual value for the electron diffraction experiment. ; _item.name '_em_electron_diffraction_phase.residual' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction_phase.highest_resolution_shell_error _item_description.description ; the highest resolution shell error in degrees. ; _item.name '_em_electron_diffraction_phase.highest_resolution_shell_error' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction_phase.overall_error _item_description.description ; the overall phase error in degrees. ; _item.name '_em_electron_diffraction_phase.overall_error' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ save__em_electron_diffraction_phase.rejection_criteria_error _item_description.description ; the rejection criteria (phase error) in degrees. ; _item.name '_em_electron_diffraction_phase.rejection_criteria_error' _item.category_id em_electron_diffraction_phase _item.mandatory_code no _item_type.code int save_ ##################################### ## EM_ELECTRON_DIFFRACTION_PATTERN ## ##################################### save_em_electron_diffraction_pattern _category.description ; data items in the em_electron_diffraction_pattern category record details about the pattern information from the electron diffraction experiment. ; _category.id em_electron_diffraction_pattern _category.mandatory_code no loop_ _category_key.name '_em_electron_diffraction_pattern.id' '_em_electron_diffraction_pattern.entry_id' loop_ _category_group.id 'inclusive_group' 'em_group' loop_ _category_examples.detail _category_examples.case ; example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub ; ; _em_electron_diffraction_pattern.entry_id 1TUB _em_electron_diffraction_pattern.id 1 _em_electron_diffraction_pattern.num_patterns_by_tilt_angle 1 _em_electron_diffraction_pattern.num_images_by_tilt_angle 4 _em_electron_diffraction_pattern.tilt_angle . ; save_ save__em_electron_diffraction_pattern.entry_id _item_description.description ; this data item is a pointer to _entry.id in the entry category. ; _item.name '_em_electron_diffraction_pattern.entry_id' _item.category_id em_electron_diffraction_pattern _item.mandatory_code yes _item_type.code code _item_linked.child_name '_em_electron_diffraction_pattern.entry_id' _item_linked.parent_name '_entry.id' save_ save__em_electron_diffraction_pattern.id _item_description.description ; the value of _electron_diffraction_pattern.id must uniquely identify the electron diffraction pattern experiment. ; _item.name '_em_electron_diffraction_pattern.id' _item.category_id em_electron_diffraction_pattern _item.mandatory_code yes _item_type.code code save_ save__em_electron_diffraction_pattern.num_patterns_by_tilt_angle _item_description.description ; the number of diffraction patterns by tilt angle. ; _item.name '_em_electron_diffraction_pattern.num_patterns_by_tilt_angle' _item.category_id em_electron_diffraction_pattern _item.mandatory_code no _item_type.code int _item_examples.case '1' save_ save__em_electron_diffraction_pattern.num_images_by_tilt_angle _item_description.description ; the number of images by tilt angle. ; _item.name '_em_electron_diffraction_pattern.num_images_by_tilt_angle' _item.category_id em_electron_diffraction_pattern _item.mandatory_code no _item_type.code int _item_examples.case '4' save_ save__em_electron_diffraction_pattern.tilt_angle _item_description.description ; the tilt angle at which the diffraction pattern was obtained. ; _item.name '_em_electron_diffraction_pattern.tilt_angle' _item.category_id em_electron_diffraction_pattern _item.mandatory_code no _item_type.code int save_ ### EOF mmcif_iims-def-2.dic ########################################################################### # # File: mmcif_pdbx-def-8.dic # # PDB Exchange Data Dictionary # # This data dictionary contains definitions used by wwPDB for data exchange # and data processing. # # Definition Section 8 # # ########################################################################### #################### ## RCSB_TABLEINFO ## #################### save_rcsb_tableinfo _category.description ; ; _category.id rcsb_tableinfo _category.mandatory_code no loop_ _category_key.name '_rcsb_tableinfo.tablename' loop_ _category_group.id 'inclusive_group' 'rcsb_group' _category_examples.case ; loop_ _rcsb_tableinfo.tablename _rcsb_tableinfo.description _rcsb_tableinfo.type _rcsb_tableinfo.table_serial_no _rcsb_tableinfo.group_name _rcsb_tableinfo.WWW_Selection_Criteria _rcsb_tableinfo.WWW_Report_Criteria summary 'summary data' 1 1 STRUCTURE 1 1 # ... ; save_ save__rcsb_tableinfo.tablename _item_description.description ; SQL table name. ; _item.name '_rcsb_tableinfo.tablename' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code code30 _item_examples.case 'structure_summary' save_ save__rcsb_tableinfo.description _item_description.description ; SQL table description. ; _item.name '_rcsb_tableinfo.description' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code text _item_examples.case 'Table of solvent coordinates' save_ save__rcsb_tableinfo.type _item_description.description ; SQL table type. ; _item.name '_rcsb_tableinfo.type' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code int _item_examples.case '0=general, 1=coordinate, 2=derived, 3=schema' save_ save__rcsb_tableinfo.table_serial_no _item_description.description ; SQL table serial number. ; _item.name '_rcsb_tableinfo.table_serial_no' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code int _item_examples.case '1,2,3,4,...' save_ save__rcsb_tableinfo.column_serial_no _item_description.description ; SQL column serial number. ; _item.name '_rcsb_tableinfo.column_serial_no' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code int _item_examples.case '1,2,3,4,...' save_ save__rcsb_tableinfo.group_name _item_description.description ; SQL table group name.. ; _item.name '_rcsb_tableinfo.group_name' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code line _item_examples.case 'STRUCTURE FEATURES, SOURCE ORGANISM' save_ save__rcsb_tableinfo.WWW_Selection_Criteria _item_description.description ; SQL table visibility in WWW selection querires. ; _item.name '_rcsb_tableinfo.WWW_Selection_Criteria' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code int _item_examples.case '0=no, 1=yes' save_ save__rcsb_tableinfo.WWW_Report_Criteria _item_description.description ; SQL table visibility in WWW reports queries. ; _item.name '_rcsb_tableinfo.WWW_Report_Criteria' _item.category_id rcsb_tableinfo _item.mandatory_code yes _item_type.code int _item_examples.case '0=no, 1=yes' save_ ##################### ## RCSB_COLUMNINFO ## ##################### save_rcsb_columninfo _category.description ; ; _category.id rcsb_columninfo _category.mandatory_code no loop_ _category_key.name '_rcsb_columninfo.tablename' '_rcsb_columninfo.columnname' loop_ _category_group.id 'inclusive_group' 'rcsb_group' _category_examples.case ; loop_ _rcsb_columninfo.tablename _rcsb_columninfo.columnname _rcsb_columninfo.description _rcsb_columninfo.example _rcsb_columninfo.type _rcsb_columninfo.table_serial_no _rcsb_columninfo.column_serial_no _rcsb_columninfo.WWW_Selection_Criteria _rcsb_columninfo.WWW_Report_Criteria summary id 'id code' 'id1, id2' 1 1 1 1 1 # ... ; save_ save__rcsb_columninfo.columnname _item_description.description ; SQL column name. ; _item.name '_rcsb_columninfo.columnname' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code code30 _item_examples.case 'id' save_ save__rcsb_columninfo.tablename _item_description.description ; SQL table name. ; _item.name '_rcsb_columninfo.tablename' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code code30 _item_examples.case 'structure_summary' save_ save__rcsb_columninfo.description _item_description.description ; SQL column description. ; _item.name '_rcsb_columninfo.description' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code text _item_examples.case 'Table of solvent coordinates' save_ save__rcsb_columninfo.example _item_description.description ; SQL column example. ; _item.name '_rcsb_columninfo.example' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code text _item_examples.case 'Table of solvent coordinates' save_ save__rcsb_columninfo.type _item_description.description ; SQL column type. ; _item.name '_rcsb_columninfo.type' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code int _item_examples.case ;1:integer, 2:float, 3:string-single-left, 4:string-single-right, 5:string-multi-left, 6:string-multi-right, 7:angle, 8:boolean, 9:single character, 10:author or atom name column, 11: Date ; save_ save__rcsb_columninfo.table_serial_no _item_description.description ; SQL table serial number. ; _item.name '_rcsb_columninfo.table_serial_no' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code int _item_examples.case '1,2,3,4,...' save_ save__rcsb_columninfo.column_serial_no _item_description.description ; SQL column serial number. ; _item.name '_rcsb_columninfo.column_serial_no' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code int _item_examples.case '1,2,3,4,...' save_ save__rcsb_columninfo.WWW_Selection_Criteria _item_description.description ; SQL column visibility in WWW selection querires. ; _item.name '_rcsb_columninfo.WWW_Selection_Criteria' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code int _item_examples.case '0=no, 1=yes' save_ save__rcsb_columninfo.WWW_Report_Criteria _item_description.description ; SQL column visibility in WWW reports queries. ; _item.name '_rcsb_columninfo.WWW_Report_Criteria' _item.category_id rcsb_columninfo _item.mandatory_code yes _item_type.code int _item_examples.case '0=no, 1=yes' save_ ## ### EOF mmcif_pdbx-def-8.dic ########################################################################### # # File: mmcif_pdbx-def-9.dic # # PDB Exchange Data Dictionary # # This data dictionary contains definitions used by RCSB for describing # derived data and computation. # # Definition Section 9 # # ########################################################################### ################# ## PDBX_DOMAIN ## ################# save_pdbx_domain _category.description ; Data items in the PDBX_DOMAIN category record information about domain definitions. A domain need not correspond to a completely polypeptide chain; it can be composed of one more more segments in a single chain, or by segments from more than one chain. ; _category.id pdbx_domain _category.mandatory_code no _category_key.name '_pdbx_domain.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _pdbx_domain.id _pdbx_domain.details d1 'Chains A, B' d2 'Asym_id D Residues 1-134' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_domain.details _item_description.description ; A description of special aspects of the structural elements that comprise a domain. ; _item.name '_pdbx_domain.details' _item.category_id pdbx_domain _item.mandatory_code no _item_type.code text _item_examples.case ; The loop between residues 18 and 23. ; save_ save__pdbx_domain.id _item_description.description ; The value of _pdbx_domain.id must uniquely identify a record in the PDBX_DOMAIN list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_pdbx_domain.id' _item.category_id pdbx_domain _item.mandatory_code yes _item_type.code code save_ ####################### ## PDBX_DOMAIN_RANGE ## ####################### save_pdbx_domain_range _category.description ; Data items in the PDBX_DOMAIN_RANGE category identify the beginning and ending points of polypeptide chain segments that form all or part of a domain. ; _category.id pdbx_domain_range _category.mandatory_code no loop_ _category_key.name '_pdbx_domain_range.domain_id' '_pdbx_domain_range.beg_label_alt_id' '_pdbx_domain_range.beg_label_asym_id' '_pdbx_domain_range.beg_label_comp_id' '_pdbx_domain_range.beg_label_seq_id' '_pdbx_domain_range.end_label_alt_id' '_pdbx_domain_range.end_label_asym_id' '_pdbx_domain_range.end_label_comp_id' '_pdbx_domain_range.end_label_seq_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _pdbx_domain_range.domain_id _pdbx_domain_range.beg_label_alt_id _pdbx_domain_range.beg_label_asym_id _pdbx_domain_range.beg_label_comp_id _pdbx_domain_range.beg_label_seq_id _pdbx_domain_range.end_label_alt_id _pdbx_domain_range.end_label_asym_id _pdbx_domain_range.end_label_comp_id _pdbx_domain_range.end_label_seq_id d1 . A PRO 1 . A GLY 29 d1 . B PRO 31 . B GLY 59 d1 . C PRO 61 . B GLY 89 d2 . D PRO 91 . D GLY 119 d2 . E PRO 121 . E GLY 149 d2 . F PRO 151 . F GLY 179 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_domain_range.beg_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_pdbx_domain_range.beg_label_alt_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_domain_range.beg_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' save_ save__pdbx_domain_range.beg_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.beg_label_asym_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_domain_range.beg_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__pdbx_domain_range.beg_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.beg_label_comp_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_domain_range.beg_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__pdbx_domain_range.beg_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.beg_label_seq_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code int _item_linked.child_name '_pdbx_domain_range.beg_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__pdbx_domain_range.beg_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.beg_auth_asym_id' _item.category_id pdbx_domain_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_domain_range.beg_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__pdbx_domain_range.beg_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.beg_auth_comp_id' _item.category_id pdbx_domain_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_domain_range.beg_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' save_ save__pdbx_domain_range.beg_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.beg_auth_seq_id' _item.category_id pdbx_domain_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_domain_range.beg_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__pdbx_domain_range.domain_id _item_description.description ; This data item is a pointer to _pdbx_domain.id in the PDBX_DOMAIN category. ; _item.name '_pdbx_domain_range.domain_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_linked.child_name '_pdbx_domain_range.domain_id' _item_linked.parent_name '_pdbx_domain.id' save_ save__pdbx_domain_range.end_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_pdbx_domain_range.end_label_alt_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_domain_range.end_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' save_ save__pdbx_domain_range.end_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.end_label_asym_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_domain_range.end_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__pdbx_domain_range.end_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.end_label_comp_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_domain_range.end_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__pdbx_domain_range.end_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.end_label_seq_id' _item.category_id pdbx_domain_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_domain_range.end_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__pdbx_domain_range.end_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.end_auth_asym_id' _item.category_id pdbx_domain_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_domain_range.end_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__pdbx_domain_range.end_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.end_auth_comp_id' _item.category_id pdbx_domain_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_domain_range.end_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' save_ save__pdbx_domain_range.end_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_domain_range.end_auth_seq_id' _item.category_id pdbx_domain_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_domain_range.end_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' save_ ######################### ## PDBX_SEQUENCE_RANGE ## ######################### save_pdbx_sequence_range _category.description ; Data items in the PDBX_SEQUENCE_RANGE category identify the beginning and ending points of polypeptide sequence segments. ; _category.id pdbx_sequence_range _category.mandatory_code no loop_ _category_key.name '_pdbx_sequence_range.seq_range_id' '_pdbx_sequence_range.beg_label_alt_id' '_pdbx_sequence_range.beg_label_asym_id' '_pdbx_sequence_range.beg_label_comp_id' '_pdbx_sequence_range.beg_label_seq_id' '_pdbx_sequence_range.end_label_alt_id' '_pdbx_sequence_range.end_label_asym_id' '_pdbx_sequence_range.end_label_comp_id' '_pdbx_sequence_range.end_label_seq_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _pdbx_sequence_range.seq_range_id _pdbx_sequence_range.beg_label_alt_id _pdbx_sequence_range.beg_label_asym_id _pdbx_sequence_range.beg_label_comp_id _pdbx_sequence_range.beg_label_seq_id _pdbx_sequence_range.end_label_alt_id _pdbx_sequence_range.end_label_asym_id _pdbx_sequence_range.end_label_comp_id _pdbx_sequence_range.end_label_seq_id s1 . A PRO 1 . A GLY 29 s2 . D PRO 91 . D GLY 119 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_sequence_range.beg_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_pdbx_sequence_range.beg_label_alt_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_sequence_range.beg_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' save_ save__pdbx_sequence_range.beg_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.beg_label_asym_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_sequence_range.beg_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__pdbx_sequence_range.beg_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.beg_label_comp_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_sequence_range.beg_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__pdbx_sequence_range.beg_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.beg_label_seq_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code int _item_linked.child_name '_pdbx_sequence_range.beg_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__pdbx_sequence_range.beg_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.beg_auth_asym_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_sequence_range.beg_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__pdbx_sequence_range.beg_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.beg_auth_comp_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_sequence_range.beg_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' save_ save__pdbx_sequence_range.beg_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.beg_auth_seq_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_sequence_range.beg_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' save_ save__pdbx_sequence_range.seq_range_id _item_description.description ; This data item is an identifier for a sequence range. ; _item.name '_pdbx_sequence_range.seq_range_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code save_ save__pdbx_sequence_range.end_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_pdbx_sequence_range.end_label_alt_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_sequence_range.end_label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' save_ save__pdbx_sequence_range.end_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.end_label_asym_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_sequence_range.end_label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__pdbx_sequence_range.end_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.end_label_comp_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_sequence_range.end_label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__pdbx_sequence_range.end_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.end_label_seq_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_sequence_range.end_label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__pdbx_sequence_range.end_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.end_auth_asym_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_sequence_range.end_auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__pdbx_sequence_range.end_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.end_auth_comp_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_sequence_range.end_auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' save_ save__pdbx_sequence_range.end_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_sequence_range.end_auth_seq_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_sequence_range.end_auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' save_ ######################## ## PDBX_FEATURE_ENTRY ## ######################## save_pdbx_feature_entry _category.description ; Data items in the PDBX_FEATURE_ENTRY category records information about properties pertaining to this structure entry. ; _category.id pdbx_feature_entry _category.mandatory_code no _category_key.name '_pdbx_feature_entry.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Gene Ontology data by entry ; ; loop_ _pdbx_feature_entry.id _pdbx_feature_entry.feature_name _pdbx_feature_entry.feature _pdbx_feature_entry.feature_type _pdbx_feature_entry.feature_assigned_by _pdbx_feature_entry.feature_citation_id 1 'molecular function' 'DNA binding activity' value GO GO 2 'biological process' 'regulation of transcription, DNA-dependent' value GO GO ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_feature_entry.id _item_description.description ; The value of _pdbx_feature_entry.id uniquely identifies a feature in the PDBX_FEATURE_ENTRY category. ; _item.name '_pdbx_feature_entry.id' _item.category_id pdbx_feature_entry _item.mandatory_code yes _item_type.code code save_ save__pdbx_feature_entry.feature_name _item_description.description ; _pdbx_feature_entry.feature_name identifies a feature by name. ; _item.name '_pdbx_feature_entry.feature_name' _item.category_id pdbx_feature_entry _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_entry.feature_type _item_description.description ; _pdbx_feature_entry.feature_type identifies the type of feature. ; _item.name '_pdbx_feature_entry.feature_type' _item.category_id pdbx_feature_entry _item.mandatory_code yes _item_type.code text loop_ _item_enumeration.value 'value' 'uri' save_ save__pdbx_feature_entry.feature _item_description.description ; The value of _pdbx_feature_entry.feature_name. ; _item.name '_pdbx_feature_entry.feature' _item.category_id pdbx_feature_entry _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_entry.feature_identifier _item_description.description ; _pdbx_feature_entry.feature_identifier is an additional identifier used to identify or accession this feature. ; _item.name '_pdbx_feature_entry.feature_identifier' _item.category_id pdbx_feature_entry _item.mandatory_code no _item_type.code text save_ save__pdbx_feature_entry.feature_assigned_by _item_description.description ; _pdbx_feature_entry.feature_assigned_by identifies the individual, organization or program that assigned the feature. ; _item.name '_pdbx_feature_entry.feature_assigned_by' _item.category_id pdbx_feature_entry _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_entry.feature_citation_id _item_description.description ; _pdbx_feature_entry.feature_citation_id is a reference to a citation in the CITATION category ; _item.name '_pdbx_feature_entry.feature_citation_id' _item.category_id pdbx_feature_entry _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_entry.feature_citation_id' _item_linked.parent_name '_citation.id' save_ save__pdbx_feature_entry.feature_software_id _item_description.description ; _pdbx_feature_entry.feature_software_id is a reference to an application described in the SOFTWARE category. ; _item.name '_pdbx_feature_entry.feature_software_id' _item.category_id pdbx_feature_entry _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_entry.feature_software_id' _item_linked.parent_name '_software.name' save_ ######################### ## PDBX_FEATURE_DOMAIN ## ######################### save_pdbx_feature_domain _category.description ; Data items in the PDBX_FEATURE_DOMAIN category records information about properties pertaining to this structure domain. ; _category.id pdbx_feature_domain _category.mandatory_code no _category_key.name '_pdbx_feature_domain.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - SCOP data for PDB Entry 1KIP domain d1kipa_ ; ; loop_ _pdbx_feature_domain.id _pdbx_feature_domain.domain_id _pdbx_feature_domain.feature_name _pdbx_feature_domain.feature _pdbx_feature_domain.feature_type _pdbx_feature_domain.feature_assigned_by _pdbx_feature_domain.feature_citation_id 1 'd1kipa_' class 'All beta proteins' value SCOP scop 2 'd1kipa_' fold 'Immunoglobulin-like beta-sandwich' value SCOP scop 3 'd1kipa_' superfamily 'Immunoglobulin' value SCOP scop 4 'd1kipa_' family 'V set domains (antibody variable domain-like)' value SCOP scop 5 'd1kipa_' domain 'Immunoglobulin light chain kappa variable domain' value SCOP scop 6 'd1kipa_' species 'Mouse (Mus musculus), cluster 4' value SCOP scop ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_feature_domain.id _item_description.description ; The value of _pdbx_feature_domain.id uniquely identifies a feature in the PDBX_FEATURE_DOMAIN category. ; _item.name '_pdbx_feature_domain.id' _item.category_id pdbx_feature_domain _item.mandatory_code yes _item_type.code code save_ save__pdbx_feature_domain.domain_id _item_description.description ; The value of _pdbx_feature_domain.id references a domain definition in category PDBX_DOMAIN. ; _item.name '_pdbx_feature_domain.domain_id' _item.category_id pdbx_feature_domain _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_feature_domain.domain_id' _item_linked.parent_name '_pdbx_domain.id' save_ save__pdbx_feature_domain.feature_name _item_description.description ; _pdbx_feature_domain.feature_name identifies a feature by name. ; _item.name '_pdbx_feature_domain.feature_name' _item.category_id pdbx_feature_domain _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_domain.feature_type _item_description.description ; _pdbx_feature_domain.feature_type identifies the type of feature. ; _item.name '_pdbx_feature_domain.feature_type' _item.category_id pdbx_feature_domain _item.mandatory_code yes _item_type.code text loop_ _item_enumeration.value 'value' 'uri' save_ save__pdbx_feature_domain.feature _item_description.description ; The value of _pdbx_feature_domain.feature_name. ; _item.name '_pdbx_feature_domain.feature' _item.category_id pdbx_feature_domain _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_domain.feature_identifier _item_description.description ; _pdbx_feature_domain.feature_identifier is an additional identifier used to identify or accession this feature. ; _item.name '_pdbx_feature_domain.feature_identifier' _item.category_id pdbx_feature_domain _item.mandatory_code no _item_type.code text save_ save__pdbx_feature_domain.feature_assigned_by _item_description.description ; _pdbx_feature_domain.feature_assigned_by identifies the individual, organization or program that assigned the feature. ; _item.name '_pdbx_feature_domain.feature_assigned_by' _item.category_id pdbx_feature_domain _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_domain.feature_citation_id _item_description.description ; _pdbx_feature_domain.feature_citation_id is a reference to a citation in the CITATION category. ; _item.name '_pdbx_feature_domain.feature_citation_id' _item.category_id pdbx_feature_domain _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_domain.feature_citation_id' _item_linked.parent_name '_citation.id' save_ save__pdbx_feature_domain.feature_software_id _item_description.description ; _pdbx_feature_domain.feature_software_id is a reference to an application described in the SOFTWARE category. ; _item.name '_pdbx_feature_domain.feature_software_id' _item.category_id pdbx_feature_domain _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_domain.feature_software_id' _item_linked.parent_name '_software.name' save_ ################################# ## PDBX_FEATURE_SEQUENCE_RANGE ## ################################# save_pdbx_feature_sequence_range _category.description ; Data items in the PDBX_FEATURE_SEQUENCE_RANGE category records information about properties pertaining to this structure sequence_range. ; _category.id pdbx_feature_sequence_range _category.mandatory_code no _category_key.name '_pdbx_feature_sequence_range.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Secondary structure computed by program DSSP. ; ; loop_ _pdbx_feature_sequence_range.id _pdbx_feature_sequence_range.seq_range_id _pdbx_feature_sequence_range.feature_name _pdbx_feature_sequence_range.feature _pdbx_feature_sequence_range.feature_type _pdbx_feature_sequence_range.feature_assigned_by _pdbx_feature_sequence_range.feature_software_id 1 H1 'secondary structure' '4-helix (alpha-helix)' value DSSP DSSP 2 T1 'secondary structure' 'hydrogen-bonded turn in beta-ladder' value DSSP DSSP ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_feature_sequence_range.id _item_description.description ; The value of _pdbx_feature_sequence_range.id uniquely identifies a feature in the PDBX_FEATURE_SEQUENCE_RANGE category ; _item.name '_pdbx_feature_sequence_range.id' _item.category_id pdbx_feature_sequence_range _item.mandatory_code yes _item_type.code code save_ save__pdbx_feature_sequence_range.seq_range_id _item_description.description ; The value of _pdbx_feature_sequence_range.seq_range_id references a sequence_range definition in category PDBX_SEQUENCE_RANGE. ; _item.name '_pdbx_feature_sequence_range.seq_range_id' _item.category_id pdbx_feature_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_feature_sequence_range.seq_range_id' _item_linked.parent_name '_pdbx_sequence_range.seq_range_id' save_ save__pdbx_feature_sequence_range.feature_name _item_description.description ; _pdbx_feature_sequence_range.feature_name identifies a feature by name. ; _item.name '_pdbx_feature_sequence_range.feature_name' _item.category_id pdbx_feature_sequence_range _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_sequence_range.feature_type _item_description.description ; _pdbx_feature_sequence_range.feature_type identifies the type of feature. ; _item.name '_pdbx_feature_sequence_range.feature_type' _item.category_id pdbx_feature_sequence_range _item.mandatory_code yes _item_type.code text loop_ _item_enumeration.value 'value' 'uri' save_ save__pdbx_feature_sequence_range.feature _item_description.description ; The value of _pdbx_feature_sequence_range.feature_name. ; _item.name '_pdbx_feature_sequence_range.feature' _item.category_id pdbx_feature_sequence_range _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_sequence_range.feature_identifier _item_description.description ; _pdbx_feature_sequence_range.feature_identifier is an additional identifier used to identify or accession this feature. ; _item.name '_pdbx_feature_sequence_range.feature_identifier' _item.category_id pdbx_feature_sequence_range _item.mandatory_code no _item_type.code text save_ save__pdbx_feature_sequence_range.feature_assigned_by _item_description.description ; _pdbx_feature_sequence_range.feature_assigned_by identifies the individual, organization or program that assigned the feature. ; _item.name '_pdbx_feature_sequence_range.feature_assigned_by' _item.category_id pdbx_feature_sequence_range _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_sequence_range.feature_citation_id _item_description.description ; _pdbx_feature_sequence_range.feature_citation_id is a reference to a citation in the CITATION category ; _item.name '_pdbx_feature_sequence_range.feature_citation_id' _item.category_id pdbx_feature_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_sequence_range.feature_citation_id' _item_linked.parent_name '_citation.id' save_ save__pdbx_feature_sequence_range.feature_software_id _item_description.description ; _pdbx_feature_sequence_range.feature_software_id is a reference to an application descripted in the SOFTWARE category. ; _item.name '_pdbx_feature_sequence_range.feature_software_id' _item.category_id pdbx_feature_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_sequence_range.feature_software_id' _item_linked.parent_name '_software.name' save_ ########################### ## PDBX_FEATURE_ASSEMBLY ## ########################### save_pdbx_feature_assembly _category.description ; Data items in the PDBX_FEATURE_ASSEMBLY category records information about properties pertaining to this structural assembly. ; _category.id pdbx_feature_assembly _category.mandatory_code no _category_key.name '_pdbx_feature_assembly.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Biological process for functional assembly ; ; loop_ _pdbx_feature_assembly.id _pdbx_feature_assembly.assembly_id _pdbx_feature_assembly.feature_name _pdbx_feature_assembly.feature _pdbx_feature_assembly.feature_type _pdbx_feature_assembly.feature_assigned_by _pdbx_feature_assembly.feature_citation_id 1 b1 'biological process' 'nitrogen metabolism' value GO GO ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_feature_assembly.id _item_description.description ; The value of _pdbx_feature_assembly.id uniquely identifies a feature in the PDBX_FEATURE_ASSEMBLY category. ; _item.name '_pdbx_feature_assembly.id' _item.category_id pdbx_feature_assembly _item.mandatory_code yes _item_type.code code save_ save__pdbx_feature_assembly.assembly_id _item_description.description ; The value of _pdbx_feature_assembly.assembly_id references an assembly definition in category STRUCT_BIOL ; _item.name '_pdbx_feature_assembly.assembly_id' _item.category_id pdbx_feature_assembly _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_feature_assembly.assembly_id' _item_linked.parent_name '_struct_biol.id' save_ save__pdbx_feature_assembly.feature_name _item_description.description ; _pdbx_feature_assembly.feature_name identifies a feature by name. ; _item.name '_pdbx_feature_assembly.feature_name' _item.category_id pdbx_feature_assembly _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_assembly.feature_type _item_description.description ; _pdbx_feature_assembly.feature_type identifies the type of feature. ; _item.name '_pdbx_feature_assembly.feature_type' _item.category_id pdbx_feature_assembly _item.mandatory_code yes _item_type.code text loop_ _item_enumeration.value 'value' 'uri' save_ save__pdbx_feature_assembly.feature _item_description.description ; The value of _pdbx_feature_assembly.feature_name. ; _item.name '_pdbx_feature_assembly.feature' _item.category_id pdbx_feature_assembly _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_assembly.feature_identifier _item_description.description ; _pdbx_feature_assembly_range.feature_identifier is an additional identifier used to identify or accession this feature. ; _item.name '_pdbx_feature_assembly.feature_identifier' _item.category_id pdbx_feature_assembly _item.mandatory_code no _item_type.code text save_ save__pdbx_feature_assembly.feature_assigned_by _item_description.description ; _pdbx_feature_assembly.feature_assigned_by identifies the individual, organization or program that assigned the feature. ; _item.name '_pdbx_feature_assembly.feature_assigned_by' _item.category_id pdbx_feature_assembly _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_assembly.feature_citation_id _item_description.description ; _pdbx_feature_assembly.feature_citation_id is a reference to a citation in the CITATION category ; _item.name '_pdbx_feature_assembly.feature_citation_id' _item.category_id pdbx_feature_assembly _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_assembly.feature_citation_id' _item_linked.parent_name '_citation.id' save_ save__pdbx_feature_assembly.feature_software_id _item_description.description ; _pdbx_feature_assembly.feature_software_id is a reference to an application described in the SOFTWARE category. ; _item.name '_pdbx_feature_assembly.feature_software_id' _item.category_id pdbx_feature_assembly _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_assembly.feature_software_id' _item_linked.parent_name '_software.name' save_ ########################## ## PDBX_FEATURE_MONOMER ## ########################## save_pdbx_feature_monomer _category.description ; Data items in the PDBX_FEATURE_MONOMER category records information about properties pertaining to particular monomers in this structure. ; _category.id pdbx_feature_monomer _category.mandatory_code no _category_key.name '_pdbx_feature_monomer.id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' 'pdbx_erf_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - ; ; loop_ _pdbx_feature_monomer.id _pdbx_feature_monomer.label_alt_id _pdbx_feature_monomer.label_asym_id _pdbx_feature_monomer.label_comp_id _pdbx_feature_monomer.label_seq_id _pdbx_feature_monomer.feature_name _pdbx_feature_monomer.feature _pdbx_feature_monomer.feature_type _pdbx_feature_monomer.feature_assigned_by _pdbx_feature_monomer.feature_citation_id 1 . A ASP 1 'SASA' 129.4 value POPS pops 1 . A ILE 2 'SASA' 35.5 value POPS pops 1 . A VAL 3 'SASA' 87.2 value POPS pops ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_feature_monomer.id _item_description.description ; The value of _pdbx_feature_monomer.id uniquely identifies a feature in the PDBX_FEATURE_MONOMER category. ; _item.name '_pdbx_feature_monomer.id' _item.category_id pdbx_feature_monomer _item.mandatory_code yes _item_type.code code save_ save__pdbx_feature_monomer.feature_name _item_description.description ; _pdbx_feature_monomer.feature_name identifies a feature by name. ; _item.name '_pdbx_feature_monomer.feature_name' _item.category_id pdbx_feature_monomer _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_monomer.feature_type _item_description.description ; _pdbx_feature_monomer.feature_type identifies the type of feature. ; _item.name '_pdbx_feature_monomer.feature_type' _item.category_id pdbx_feature_monomer _item.mandatory_code yes _item_type.code text loop_ _item_enumeration.value 'value' 'uri' save_ save__pdbx_feature_monomer.feature _item_description.description ; The value of _pdbx_feature_monomer.feature_name. ; _item.name '_pdbx_feature_monomer.feature' _item.category_id pdbx_feature_monomer _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_monomer.feature_identifier _item_description.description ; _pdbx_feature_monomer.feature_identifier is an additional identifier used to identify or accession this feature. ; _item.name '_pdbx_feature_monomer.feature_identifier' _item.category_id pdbx_feature_monomer _item.mandatory_code no _item_type.code text save_ save__pdbx_feature_monomer.feature_assigned_by _item_description.description ; _pdbx_feature_monomer.feature_assigned_by identifies the individual, organization or program that assigned the feature. ; _item.name '_pdbx_feature_monomer.feature_assigned_by' _item.category_id pdbx_feature_monomer _item.mandatory_code yes _item_type.code text save_ save__pdbx_feature_monomer.feature_citation_id _item_description.description ; _pdbx_feature_monomer.feature_citation_id is a reference to a citation in the CITATION category. ; _item.name '_pdbx_feature_monomer.feature_citation_id' _item.category_id pdbx_feature_monomer _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.feature_citation_id' _item_linked.parent_name '_citation.id' save_ save__pdbx_feature_monomer.feature_software_id _item_description.description ; _pdbx_feature_monomer.feature_software_id is a reference to an application described in the SOFTWARE category. ; _item.name '_pdbx_feature_monomer.feature_software_id' _item.category_id pdbx_feature_monomer _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.feature_software_id' _item_linked.parent_name '_software.name' save_ ## save__pdbx_feature_monomer.label_alt_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_pdbx_feature_monomer.label_alt_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.label_alt_id' _item_linked.parent_name '_atom_site.label_alt_id' save_ save__pdbx_feature_monomer.label_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_feature_monomer.label_asym_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__pdbx_feature_monomer.label_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_feature_monomer.label_comp_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__pdbx_feature_monomer.label_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_feature_monomer.label_seq_id' _item.category_id pdbx_sequence_range _item.mandatory_code yes _item_type.code int _item_linked.child_name '_pdbx_feature_monomer.label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__pdbx_feature_monomer.auth_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_pdbx_feature_monomer.auth_asym_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.auth_asym_id' _item_linked.parent_name '_atom_site.auth_asym_id' save_ save__pdbx_feature_monomer.auth_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_pdbx_feature_monomer.auth_comp_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.auth_comp_id' _item_linked.parent_name '_atom_site.auth_comp_id' save_ save__pdbx_feature_monomer.auth_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_pdbx_feature_monomer.auth_seq_id' _item.category_id pdbx_sequence_range _item.mandatory_code no _item_type.code code _item_linked.child_name '_pdbx_feature_monomer.auth_seq_id' _item_linked.parent_name '_atom_site.auth_seq_id' save_ ## ## End of file: mmcif_pdbx-def-9.dic ## ########################################################################### # # File: mmcif_pdbx-def-10.dic # # PDB Exchange Data Dictionary # # This data dictionary contains preliminary extensions for describing # macromolecular powder diffraction experiments. # # Definition Section 10 # # ########################################################################### save__diffrn_radiation.pdbx_analyzer _item_description.description ; Indicates the method used to obtain monochromatic radiation. _diffrn_radiation.monochromator describes the primary beam monochromator (pre-specimen monochromation). _diffrn_radiation.pdbx_analyzer specifies the post-diffraction analyser (post-specimen) monochromation. Note that monochromators may have either 'parallel' or 'antiparallel' orientation. It is assumed that the geometry is parallel unless specified otherwise. In a parallel geometry, the position of the monochromator allows the incident beam and the final post-specimen and post-monochromator beam to be as close to parallel as possible. In a parallel geometry, the diffracting planes in the specimen and monochromator will be parallel when 2*theta(monochromator) is equal to 2*theta (specimen). For further discussion see R. Jenkins and R. Snyder, Introduction to X-ray Powder Diffraction, Wiley (1996), pp. 164-5. ; _item.name '_diffrn_radiation.pdbx_analyzer' _item.category_id diffrn_radiation _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'GE(111)' 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite (0001)' 'Si (111), antiparallel' _item_aliases.dictionary cif_pd.dic _item_aliases.version 1.0 _item_aliases.alias_name '_pd_instr_monochr_post_spec' save_ save_pdbx_exptl_pd _category.description ; Data items in the pdbx_exptl_pd record information about powder sample preparations. ; _category.id pdbx_exptl_pd _category.mandatory_code no _category_key.name '_pdbx_exptl_pd.entry_id' loop_ _category_group.id 'inclusive_group' 'pdbx_group' save_ save__pdbx_exptl_pd.entry_id _item_description.description ; The value of _pdbx_exptl_pd.entry_id uniquely identifies a record in the PDBX_EXPTL_PD category. ; _item.name '_pdbx_exptl_pd.entry_id' _item.category_id pdbx_exptl_pd _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_exptl_pd.entry_id' _item_linked.parent_name '_entry.id' save_ save__pdbx_exptl_pd.spec_preparation_pH _item_description.description ; The pH at which the powder sample was prepared. ; _item.name '_pdbx_exptl_pd.spec_preparation_pH' _item.category_id pdbx_exptl_pd _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__pdbx_exptl_pd.spec_preparation_pH_range _item_description.description ; The range of pH values at which the sample was prepared. Used when a point estimate of pH is not appropriate. ; _item.name '_pdbx_exptl_pd.spec_preparation_pH_range' _item.category_id pdbx_exptl_pd _item.mandatory_code no _item_type.code line loop_ _item_examples.case '5.6 - 6.4' save_ save__pdbx_exptl_pd.spec_preparation _item_description.description ; A description of preparation steps for producing the diffraction specimen from the sample. Include any procedures related to grinding, sieving, spray drying, etc. ; _item.name '_pdbx_exptl_pd.spec_preparation' _item.category_id pdbx_exptl_pd _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'POLYCRYSTAL SLURRY' 'wet grinding in acetone' 'sieved through a 44 micron (325 mesh/inch) sieve' 'spray dried in water with 1% clay' _item_aliases.dictionary cif_pd.dic _item_aliases.version 1.0 _item_aliases.alias_name '_pd_spec_preparation' save_ save__refine.pdbx_pd_number_of_powder_patterns _item_description.description ; The total number of powder patterns used. ; _item.name '_refine.pdbx_pd_number_of_powder_patterns' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.pdbx_pd_number_of_points _item_description.description ; The total number of data points in the processed diffractogram. ; _item.name '_refine.pdbx_pd_number_of_points' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int _item_aliases.dictionary cif_pd.dic _item_aliases.version 1.0 _item_aliases.alias_name '_pd_proc_number_of_points' save_ save__refine.pdbx_pd_meas_number_of_points _item_description.description ; The total number of points in the measured diffractogram. ; _item.name '_refine.pdbx_pd_meas_number_of_points' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int _item_aliases.dictionary cif_pd.dic _item_aliases.version 1.0 _item_aliases.alias_name '_pd_meas_number_of_points' save_ save__refine.pdbx_pd_proc_ls_prof_R_factor _item_description.description ; Rietveld/Profile fit R factors. Note that the R factor computed for Rietveld refinements using the extracted reflection intensity values (often called the Rietveld or Bragg R factor, R~B~) is not properly a profile R factor. pdbx_pd_proc_ls_prof_R_factor, often called R~p~, is an unweighted fitness metric for the agreement between the observed and computed diffraction patterns R~p~ = sum~i~ | I~obs~(i) - I~calc~(i) | / sum~i~ ( I~obs~(i) ) Note that in the above equations, w(i) is the weight for the ith data point I~obs~(i) is the observed intensity for the ith data point, sometimes referred to as y~i~(obs) or y~oi~. I~calc~(i) is the computed intensity for the ith data point with background and other corrections applied to match the scale of the observed dataset, sometimes referred to as y~i~(calc) or y~ci~. n is the total number of data points (see _refine.pdbx_pd_number_of_points) less the number of data points excluded from the refinement. p is the total number of refined parameters. ; _item.name '_refine.pdbx_pd_proc_ls_prof_R_factor' _item.category_id refine _item.mandatory_code no _item_type.code float _item_aliases.dictionary cif_pd.dic _item_aliases.version 1.0 _item_aliases.alias_name '_pd_proc_ls_prof_R_factor' save_ save__refine.pdbx_pd_proc_ls_prof_wR_factor _item_description.description ; Rietveld/Profile fit R factors. Note that the R factor computed for Rietveld refinements using the extracted reflection intensity values (often called the Rietveld or Bragg R factor, R~B~) is not properly a profile R factor. pdbx_pd_proc_ls_prof_wR_factor often called R~wp~, is a weighted fitness metric for the agreement between the observed and computed diffraction patterns R~wp~ = SQRT { sum~i~ ( w(i) [ I~obs~(i) - I~calc~(i) ]^2^ ) / sum~i~ ( w(i) [I~obs~(i)]^2^ ) } Note that in the above equations, w(i) is the weight for the ith data point I~obs~(i) is the observed intensity for the ith data point, sometimes referred to as y~i~(obs) or y~oi~. I~calc~(i) is the computed intensity for the ith data point with background and other corrections applied to match the scale of the observed dataset, sometimes referred to as y~i~(calc) or y~ci~. n is the total number of data points (see _refine.pdbx_pd_number_of_points) less the number of data points excluded from the refinement. p is the total number of refined parameters. ; _item.name '_refine.pdbx_pd_proc_ls_prof_wR_factor' _item.category_id refine _item.mandatory_code no _item_type.code float _item_aliases.dictionary cif_pd.dic _item_aliases.version 1.0 _item_aliases.alias_name '_pd_proc_ls_prof_wR_factor' save_ save__refine.pdbx_pd_Marquardt_correlation_coeff _item_description.description ; The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. This correlation factor is found in the fitting using the Levenberg-Marquardt algorithm to search for the minimum value of chisquare. Almost all computer codes for Rietveld refinement employ the Gauss-Newton algorithm to find parameters which minimize the weighted sum of squares of the residuals. A description of the equations is given on http://www.water.hut.fi/~tkarvone/fr_org_s.htm ; _item.name '_refine.pdbx_pd_Marquardt_correlation_coeff' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.pdbx_pd_Fsqrd_R_factor _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. sum|F~obs~**2 - F~calc~**2| R = --------------------- sum|F~obs~**2| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.pdbx_pd_Fsqrd_R_factor' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 _item_type.code float save_ save__refine.pdbx_pd_ls_matrix_band_width _item_description.description ; The least squares refinement "band matrix" approximation to the full matrix. ; _item.name '_refine.pdbx_pd_ls_matrix_band_width' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ ### EOF mmcif_pdbx-def-10.dic ####################### ## PDBX_SOLN_SCATTER ## ####################### save_pdbx_soln_scatter _category.description ; Data items in the PDBX_SOLN_SCATTER category record details about a solution scattering experiment ; _category.id pdbx_soln_scatter _category.mandatory_code no loop_ _category_key.name '_pdbx_soln_scatter.entry_id' '_pdbx_soln_scatter.id' loop_ _category_group.id 'inclusive_group' 'solution_scattering_group' loop_ _category_examples.detail _category_examples.case ; Example 1 - based on PDB entry 1HAQ ; ; loop_ _pdbx_soln_scatter.entry_id _pdbx_soln_scatter.id _pdbx_soln_scatter.type _pdbx_soln_scatter.source_type _pdbx_soln_scatter.source_class _pdbx_soln_scatter.source_beamline _pdbx_soln_scatter.source_beamline_instrument _pdbx_soln_scatter.detector_specific _pdbx_soln_scatter.detector_type _pdbx_soln_scatter.temperature _pdbx_soln_scatter.pH _pdbx_soln_scatter.num_time_frames _pdbx_soln_scatter.concentration_range _pdbx_soln_scatter.buffer_name _pdbx_soln_scatter.mean_guiner_radius _pdbx_soln_scatter.mean_guiner_radius_esd _pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration _pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd _pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration _pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_eds _pdbx_soln_scatter.protein_length 1HAQ 1 x-ray 'SRS BEAMLINE 2.1' 'synchrotron' '2.1' . . '500-channel quadrant' 288 . 10 '0.7 - 14' tris 11.1 0.4 4.4 0.2 1.7 0.1 40 1HAQ 2 neutron 'ILL' 'neutron source' . 'D11, D22' . 'area' . . . '0.4 - 9.6' 'PBS in 99.9% D2O' 11.3 0.4 3.9 0.2 1.51 0.06 '37.0 - 39.0' 1HAQ 3 neutron 'ISIS' 'neutron source' 'Pulsed Neutron' 'LOQ' . 'AREA (TIME-OF-FLIGHT)' . . . '3.7, 6.1' 'PBS in 99.9% D2O' 11.7 0.5 . . . . 40.0 ; save_ save__pdbx_soln_scatter.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_pdbx_soln_scatter.entry_id' _item.category_id pdbx_soln_scatter _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_soln_scatter.entry_id' _item_linked.parent_name '_entry.id' save_ save__pdbx_soln_scatter.id _item_description.description ; The value of _pdbx_soln_scatter.id must uniquely identify the sample in the category PDBX_SOLN_SCATTER ; _item.name '_pdbx_soln_scatter.id' _item.category_id pdbx_soln_scatter _item.mandatory_code yes _item_type.code code save_ save__pdbx_soln_scatter.type _item_description.description ; The type of solution scattering experiment carried out ; _item.name '_pdbx_soln_scatter.type' _item.category_id pdbx_soln_scatter _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value 'x-ray' 'neutron' 'modelling' save_ save__pdbx_soln_scatter.source_beamline _item_description.description ; The beamline name used for the experiment ; _item.name '_pdbx_soln_scatter.source_beamline' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text save_ save__pdbx_soln_scatter.source_beamline_instrument _item_description.description ; The instrumentation used on the beamline ; _item.name '_pdbx_soln_scatter.source_beamline_instrument' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text save_ save__pdbx_soln_scatter.detector_type _item_description.description ; The general class of the radiation detector. ; _item.name '_pdbx_soln_scatter.detector_type' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text save_ save__pdbx_soln_scatter.detector_specific _item_description.description ; The particular radiation detector. In general this will be a manufacturer, description, model number or some combination of these. ; _item.name '_pdbx_soln_scatter.detector_specific' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text save_ save__pdbx_soln_scatter.source_type _item_description.description ; The make, model, name or beamline of the source of radiation. ; _item.name '_pdbx_soln_scatter.source_type' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text save_ save__pdbx_soln_scatter.source_class _item_description.description ; The general class of the radiation source. ; _item.name '_pdbx_soln_scatter.source_class' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'neutron source' 'synchrotron' save_ save__pdbx_soln_scatter.num_time_frames _item_description.description ; The number of time frame solution scattering images used. ; _item.name '_pdbx_soln_scatter.num_time_frames' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code int save_ save__pdbx_soln_scatter.sample_pH _item_description.description ; The pH value of the buffered sample. ; _item.name '_pdbx_soln_scatter.sample_pH' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code float save_ save__pdbx_soln_scatter.temperature _item_description.description ; The temperature in kelvins at which the experiment was conducted ; _item.name '_pdbx_soln_scatter.temperature' _item.category_id pdbx_soln_scatter _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code kelvins save_ save__pdbx_soln_scatter.concentration_range _item_description.description ; The concentration range (mg/mL) of the complex in the sample used in the solution scattering experiment to determine the mean radius of structural elongation. ; _item.name '_pdbx_soln_scatter.concentration_range' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code line _item_units.code mg_per_ml _item_examples.case '0.7 - 14' save_ save__pdbx_soln_scatter.buffer_name _item_description.description ; The name of the buffer used for the sample in the solution scattering experiment. ; _item.name '_pdbx_soln_scatter.buffer_name' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code line _item_examples.case 'acetic acid' save_ save__pdbx_soln_scatter.mean_guiner_radius _item_description.description ; The mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q gives the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 ; _item.name '_pdbx_soln_scatter.mean_guiner_radius' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_units.code nanometres _item_type.code float _item_related.related_name '_pdbx_soln_scatter.mean_guiner_radius_esd' _item_related.function_code associated_esd save_ save__pdbx_soln_scatter.mean_guiner_radius_esd _item_description.description ; The estimated standard deviation for the mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 ; _item.name '_pdbx_soln_scatter.mean_guiner_radius_esd' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_related.related_name '_pdbx_soln_scatter.mean_guiner_radius' _item_related.function_code associated_value save_ save__pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration _item_description.description ; The minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 ; _item.name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_related.related_name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd' _item_related.function_code associated_esd save_ save__pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd _item_description.description ; The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 ; _item.name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_related.related_name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration' _item_related.function_code associated_value save_ save__pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration _item_description.description ; The maximum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 ; _item.name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_related.related_name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd' _item_related.function_code associated_esd save_ save__pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd _item_description.description ; The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 ; _item.name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code float _item_units.code nanometres _item_related.related_name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration' _item_related.function_code associated_value save_ save__pdbx_soln_scatter.protein_length _item_description.description ; The length (or range) of the protein sample under study. If the solution structure is approximated as an elongated elliptical cyclinder the the length L is determined from, L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ] The length should also be given by L = pi I(0) / [ I(Q).Q]_Q->0 ; _item.name '_pdbx_soln_scatter.protein_length' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code line save_ save__pdbx_soln_scatter.data_reduction_software_list _item_description.description ; A list of the software used in the data reduction ; _item.name '_pdbx_soln_scatter.data_reduction_software_list' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text _item_examples.case 'OTOKO' save_ save__pdbx_soln_scatter.data_analysis_software_list _item_description.description ; A list of the software used in the data analysis ; _item.name '_pdbx_soln_scatter.data_analysis_software_list' _item.category_id pdbx_soln_scatter _item.mandatory_code no _item_type.code text _item_examples.case 'SCTPL5 GNOM' save_ ############################# ## PDBX_SOLN_SCATTER_MODEL ## ############################# save_pdbx_soln_scatter_model _category.description ; Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the homology model fitting to the solution scatter data. ; _category.id pdbx_soln_scatter_model _category.mandatory_code no loop_ _category_key.name '_pdbx_soln_scatter_model.id' '_pdbx_soln_scatter_model.scatter_id' loop_ _category_group.id 'inclusive_group' 'solution_scattering_group' save_ save__pdbx_soln_scatter_model.scatter_id _item_description.description ; This data item is a pointer to _pdbx_soln_scatter.id in the PDBX_SOLN_SCATTER category. ; _item.name '_pdbx_soln_scatter_model.scatter_id' _item.category_id pdbx_soln_scatter_model _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_soln_scatter_model.scatter_id' _item_linked.parent_name '_pdbx_soln_scatter.id' save_ save__pdbx_soln_scatter_model.id _item_description.description ; The value of _pdbx_soln_scatter_model.id must uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL ; _item.name '_pdbx_soln_scatter_model.id' _item.category_id pdbx_soln_scatter_model _item.mandatory_code yes _item_type.code code save_ save__pdbx_soln_scatter_model.details _item_description.description ; A description of any additional details concerning the experiment. ; _item.name '_pdbx_soln_scatter_model.details' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code text _item_examples.case ; Homology models were built for the 17 SCR domains and energy minimisations were performed to improve the connectivity in the fh model. triantennary complex-type carbohydrate structures (MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the N-linked glycosylation sites. a library of linker peptide conformations was used in domain modelling constrained by the solution scattering fits. modelling with the scattering data was also carried out by rotational search methods. the x-ray and neutron scattering curve I(Q) was calculated assuming a uniform scattering density for the spheres using the debye equation as adapted to spheres. x-ray curves were calculated from the hydrated sphere models without corrections for wavelength spread or beam divergence, while these corrections were applied for the neutron curves but now using unhydrated models. ; save_ save__pdbx_soln_scatter_model.method _item_description.description ; A description of the methods used in the modelling ; _item.name '_pdbx_soln_scatter_model.method' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code text _item_examples.case ; Constrained scattering fitting of homology models ; save_ save__pdbx_soln_scatter_model.software_list _item_description.description ; A list of the software used in the modeeling ; _item.name '_pdbx_soln_scatter_model.software_list' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code text _item_examples.case ; INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI ; save_ save__pdbx_soln_scatter_model.software_author_list _item_description.description ; A list of the software authors ; _item.name '_pdbx_soln_scatter_model.software_author_list' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code text _item_examples.case ; MSI ; save_ save__pdbx_soln_scatter_model.entry_fitting_list _item_description.description ; A list of the entries used to fit the model to the scattering data ; _item.name '_pdbx_soln_scatter_model.entry_fitting_list' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code text _item_examples.case ; PDB CODE 1HFI, 1HCC, 1HFH, 1VCC ; save_ save__pdbx_soln_scatter_model.num_conformers_calculated _item_description.description ; The number of model conformers calculated. ; _item.name '_pdbx_soln_scatter_model.num_conformers_calculated' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code int save_ save__pdbx_soln_scatter_model.num_conformers_submitted _item_description.description ; The number of model conformers submitted in the entry ; _item.name '_pdbx_soln_scatter_model.num_conformers_submitted' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code int save_ save__pdbx_soln_scatter_model.conformer_selection_criteria _item_description.description ; A description of the conformer selection criteria used. ; _item.name '_pdbx_soln_scatter_model.conformer_selection_criteria' _item.category_id pdbx_soln_scatter_model _item.mandatory_code no _item_type.code text _item_examples.case ; The modelled scattering curves were assessed by calculation of the RG, RSX-1 and RXS-2 values in the same Q ranges used in the experimental Guinier fits. models were then ranked using a goodness-of-fit R-factor defined by analogy with protein crystallography and based on the experimental curves in the Q range extending to 1.4 nm-1. ; save_ ## ##