International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 144-198
https://doi.org/10.1107/97809553602060000738

Chapter 3.6. Classification and use of macromolecular data

Chapter index

absolute configuration 3.6.7.2.2, 3.6.7.2.3
ambient conditions
mmCIF 3.6.5.2
_atom_site_label 3.6.7.1.1, 3.6.7.1.1
_atom_site.auth_seq_id 3.6.7.1.1
_atom_site.B_iso_or_equiv 3.6.7.1.1
_atom_site.disorder_assembly 3.6.7.1.4
_atom_site.disorder_group 3.6.7.1.4
_atom_site.footnote_id 3.6.7.1.1, 3.6.7.1.2
_atom_site.group_PDB 3.6.7.1.1
_atom_site.label_alt_id 3.6.3, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.4
_atom_site.label_asym_id 3.6.3, 3.6.7.1.1
_atom_site.label_atom_id 3.6.7.1.1
_atom_site.label_comp_id 3.6.3, 3.6.7.1.1, 3.6.7.5.7
_atom_site.label_entity_id 3.6.7.1.1
_atom_site.label_seq_id 3.6.7.1.1
_atom_site.type_symbol 3.6.7.1.1
ATOM_SITE_ANISOTROP 3.6.7.1, 3.6.7.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.1
_atom_site_anisotrop.id 3.6.7.1.1
_atom_sites.entry_id 3.6.7.1.2
_atom_sites_footnote.id 3.6.7.1.1
atom properties
atom sites
alternative conformations 3.6.7.1.4
anisotropic displacement parameters 3.6.7.1.1, 3.6.7.1.1
isotropic displacement parameters 3.6.7.1.1
mmCIF 3.6.7.1
occupancy 3.6.3
positional coordinates 3.6.7.1.1
_audit_block_code 3.6.9.1
_audit.revision_id 3.6.9.1
AUDIT_AUTHOR 3.6.9, 3.6.9.1, 3.6.9.1
AUDIT_CONFORM 3.6.9, 3.6.9.1, 3.6.9.1
AUDIT_CONTACT_AUTHOR 3.6.9, 3.6.9.1, 3.6.9.1
_audit_link.block_description 3.6.9.2
biological function 3.6.3
BioMagResBank A3.6.2.3.1
bond angle 3.6.7.2.2, 3.6.7.2.3
bond distance 3.6.7.2.2, 3.6.7.2.3
bond order 3.6.7.2.2, 3.6.7.2.3
bond type 3.6.7.2.2
bond valence 3.6.7.7
Cambridge Structural Database 3.6.7.2.2
category group
mmCIF 3.6.4
_cell_length_a 3.6.1
_cell.entry_id 3.6.9.2
_cell.length_a 3.6.1
CELL_MEASUREMENT 3.6.5.1, 3.6.5.1, 3.6.5.1, 3.6.5.1
CELL_MEASUREMENT_REFLN 3.6.5.1, 3.6.5.1, 3.6.5.1, 3.6.5.1
_chem_comp.id 3.6.7.1.1
_chem_comp.model_details 3.6.7.2.2, 3.6.7.2.2
_chem_comp.model_erf 3.6.7.2.2, 3.6.7.2.2
_chem_comp.model_source 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.2
_chem_comp.one_letter_code 3.6.7.2.2
_chem_comp.three_letter_code 3.6.7.2.2
_chem_comp.type 3.6.7.2.2, 3.6.7.2.2
CHEM_COMP_ANGLE 3.6.7.2, 3.6.7.2.2, 3.6.7.2.2
_chem_comp_atom.atom_id 3.6.7.1.1
CHEM_COMP_CHIR_ATOM 3.6.7.2, 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.3
CHEM_COMP_LINK 3.6.7.2, 3.6.7.2.2, 3.6.7.2.2
_chem_comp_link.link_id 3.6.7.2.2
CHEM_COMP_PLANE_ATOM 3.6.7.2, 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.3
CHEM_COMP_TOR_VALUE 3.6.7.2, 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.2
CHEM_LINK_CHIR 3.6.7.2, 3.6.7.2.3, 3.6.7.2.3
CHEM_LINK_CHIR_ATOM 3.6.7.2, 3.6.7.2.3, 3.6.7.2.3
CHEM_LINK_PLANE 3.6.7.2, 3.6.7.2.3, 3.6.7.2.3
CHEM_LINK_PLANE_ATOM 3.6.7.2, 3.6.7.2.3, 3.6.7.2.3
CHEM_LINK_TOR 3.6.7.2, 3.6.7.2.3, 3.6.7.2.3
CHEM_LINK_TOR_VALUE 3.6.7.2, 3.6.7.2.3, 3.6.7.2.3
CHEMICAL_CONN_ATOM 3.6.7.2, 3.6.7.2.1, 3.6.7.2.1
CHEMICAL_CONN_BOND 3.6.7.2, 3.6.7.2.1, 3.6.7.2.1
_chemical_conn_bond.type 3.6.7.2.2
CHEMICAL_FORMULA 3.6.7.2, 3.6.7.2.1, 3.6.7.2.1
_chemical_formula.entry_id 3.6.7.2.1
chemical components (mmCIF) 3.6.7.2.2
chemical entity
mmCIF 3.6.7.2.2
chemical species, handling in mmCIF 3.6.7.2
chemistry 3.6.2
mmCIF 3.6.7
chiral volume 3.6.7.2.2, 3.6.7.2.3
CIFTr A3.6.2.4
_citation.id 3.6.8.2
CITATION_AUTHOR 3.6.8.1, 3.6.8.1, 3.6.8.1, 3.6.8.1
CITATION_EDITOR 3.6.8.1, 3.6.8.1, 3.6.8.1, 3.6.8.1
citation
of database entries 3.6.8.3
of scientific literature 3.6.8.1
of software 3.6.8.2
computer programs
CIFTr A3.6.2.4
PDB_EXTRACT A3.6.2.4
PROTIN/PROLSQ 3.6.6.2.3
RESTRAIN 3.6.6.2.3
_computing.entry_id 3.6.8.2
connectivity
structural interactions (mmCIF) 3.6.7.5.3
coreCIF
embedded in mmCIF dictionary 3.6.1
crambin (mmCIF example structure) 3.6.3
Cruickshank diffraction-component precision index 3.6.6.2.1
cryo-electron microscopy A3.6.2.3, A3.6.2.3.2
crystal
characterization 3.6.5.3
_database_2.database_code 3.6.8.3.1, 3.6.8.3.1
_database_2.database_id 3.6.8.3.1, 3.6.8.3.1
DATABASE_PDB_CAVEAT 3.6.8.3, 3.6.8.3.2, 3.6.8.3.2, 3.6.9.3
DATABASE_PDB_MATRIX 3.6.8.3, 3.6.8.3.2, 3.6.8.3.2, 3.6.9.3
DATABASE_PDB_REMARK 3.6.8.3, 3.6.8.3.2, 3.6.8.3.2, 3.6.9.3
_database_pdb_remark.id 3.6.8.3.2
DATABASE_PDB_REV 3.6.8.3, 3.6.8.3.2, 3.6.8.3.2, 3.6.9.3
DATABASE_PDB_REV_RECORD 3.6.8.3, 3.6.8.3.2, 3.6.8.3.2, 3.6.9.3
DATABASE_PDB_TVECT 3.6.8.3, 3.6.8.3.2, 3.6.8.3.2, 3.6.9.3
database
entries 3.6.7.5.6
data block
history 3.6.9.1
intra-file relationship 3.6.9
data collection
mmCIF data items 3.6.5.2
data exchange standards
data name
alias 3.6.1
correspondence between coreCIF and mmCIF 3.6.1
DDL1 (Dictionary Definition Language)
_type_conditions 3.6.4
DDL2 (Dictionary Definition Language)
_item_aliases.alias_name 3.6.1
DDL2
history 3.6.1
use in mmCIF 3.6.1
dictionary
mmCIF 3.6.1
PDB exchange (pdbx) A3.6.2
diffraction experiment, overview 3.6.5.2
DIFFRN_ATTENUATOR 3.6.5.2, 3.6.5.2
DIFFRN_DETECTOR 3.6.5.2, 3.6.5.2, 3.6.5.2
_diffrn_detector.diffrn_id 3.6.5.2
DIFFRN_MEASUREMENT 3.6.5.2, 3.6.5.2
DIFFRN_ORIENT_MATRIX 3.6.5.2, 3.6.5.2
DIFFRN_ORIENT_REFLN 3.6.5.2, 3.6.5.2
DIFFRN_RADIATION 3.6.5.2, 3.6.5.2
DIFFRN_RADIATION_WAVELENGTH 3.6.5.2, 3.6.5.2
DIFFRN_REFLN 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2
_diffrn_refln_index_h 3.6.5.2
_diffrn_refln.diffrn_id 3.6.5.2
_diffrn_refln.id 3.6.5.2
DIFFRN_REFLNS 3.6.5.2, 3.6.5.2, 3.6.5.2
DIFFRN_REFLNS_CLASS 3.6.5.2, 3.6.5.2, 3.6.6.3.2
DIFFRN_SCALE_GROUP 3.6.5.2
DIFFRN_SOURCE 3.6.5.2, 3.6.5.2, 3.6.5.2
DIFFRN_STANDARD_REFLN 3.6.5.2, 3.6.5.2
DIFFRN_STANDARDS 3.6.5.2, 3.6.5.2
disorder 3.6.6.2.2
disulfide link 3.6.3, 3.6.7.5.3, 3.6.7.5.3
ENTITY_KEYWORDS 3.6.7.3, 3.6.7.3.1, 3.6.7.3.2
_entity_link.link_id 3.6.7.2.3
_entity_name_sys.system 3.6.7.3.1
_entity_poly.nstd_chirality 3.6.7.3.2
_entity_poly.nstd_linkage 3.6.7.3.2
_entity_poly.nstd_monomer 3.6.7.3.2
_entity_poly.type_details 3.6.7.3.2
_entity_poly_seq.mon_id 3.6.3, 3.6.7.3.2
_entity_poly_seq.num 3.6.7.1.1
European Bioinformatics Institute A3.6.2
experimental measurements
mmCIF data items 3.6.5
EXPTL_CRYSTAL_FACE 3.6.5.3, 3.6.5.3, 3.6.5.3.1
EXPTL_CRYSTAL_GROW 3.6.5, 3.6.5.3, 3.6.5.3, 3.6.5.3.2
_exptl_crystal_grow.details 3.6.5.3.2
_exptl_crystal_grow.method 3.6.5.3.2
_exptl_crystal_grow.method_ref 3.6.5.3.2
_exptl_crystal_grow.pH 3.6.5.3.2
EXPTL_CRYSTAL_GROW_COMP 3.6.5, 3.6.5.3, 3.6.5.3, 3.6.5.3.2, 3.6.5.3.2, 3.6.5.3.2
_exptl_crystal_grow_comp.sol_id 3.6.5.3.2
external reference file
standard chemical data for monomers 3.6.7.2.2
genetically manipulated source of biological macromolecules 3.6.7.3.1
GEOM_ANGLE 3.6.7.4, 3.6.7.4
GEOM_BOND 3.6.7.4, 3.6.7.4
GEOM_CONTACT 3.6.7.4, 3.6.7.4
GEOM_HBOND 3.6.7.4, 3.6.7.4
GEOM_TORSION 3.6.7.4, 3.6.7.4
geometry 3.6.7.2.2, 3.6.7.4
hydrogen bond 3.6.7.5.3, 3.6.7.5.7
intensity measurements 3.6.5.2
excluded from refinement 3.6.6.2.1
threshold 3.6.6.2.1, 3.6.6.3.2
units (mmCIF) 3.6.6.3.1
used in refinement 3.6.6.3
International Structural Genomics Organization A3.6.2
intramolecular geometry 3.6.7.2.3
IUCr A3.6.2
JOURNAL_INDEX 3.6.8.4, 3.6.8.4.1, 3.6.8.4.1
keywords 3.6.7.5.8
macromolecular structure 3.6.3, 3.6.7.5
biological units 3.6.7.5.1
secondary structure 3.6.7.5.2
metadata 3.6.9
mmCIF
atom properties 3.6.7
category groups 3.6.4, 3.6.4.1
chemistry 3.6.7
classification and use 3.6.1
data collection 3.6.5.2
design considerations 3.6.2
experimental measurements 3.6.5
history 3.6.1
list of categories A3.6.1.1
refinement 3.6.6.2, 3.6.6.2.5
relation to PDB format 3.6.8.3.2
structural model 3.6.3, 3.6.7
structure analysis 3.6.6
use in PDB data management A3.6.2
molecular chemistry, differences between coreCIF and mmCIF 3.6.7.2.1
monomer components of biological macromolecules 3.6.7.2.2
natural tissue, source of biological macromolecules 3.6.7.3.1
NMRStar A3.6.2.3.1
NMR structures 3.6.7.1.4, A3.6.2.3.1
noncrystallographic symmetry 3.6.6.1.2, 3.6.6.2.3, 3.6.6.2.3, 3.6.7.5.5
PDB_EXTRACT A3.6.2.4
phasing 3.6.6.1
characterization of data sets 3.6.6.1.3, 3.6.6.1.6
isomorphous replacement 3.6.6.1.3
molecular averaging 3.6.6.1.2
PHASING_AVERAGING 3.6.6.1, 3.6.6.1.2, 3.6.6.1.2, 3.6.6.1.2
PHASING_ISOMORPHOUS 3.6.6.1, 3.6.6.1.3, 3.6.6.1.3
_phasing_isomorphous.method 3.6.6.1.3
PHASING_MAD_CLUST 3.6.6.1, 3.6.6.1.4, 3.6.6.1.4
PHASING_MAD_EXPT 3.6.6.1, 3.6.6.1.4, 3.6.6.1.4
PHASING_MAD_RATIO 3.6.6.1, 3.6.6.1.4, 3.6.6.1.4
_phasing_mad_ratio.d_res_high 3.6.6.1.4
_phasing_mad_ratio.d_res_low 3.6.6.1.4
PHASING_MAD_SET 3.6.6.1, 3.6.6.1.4, 3.6.6.1.4
PHASING_MIR_DER 3.6.6.1, 3.6.6.1.5, 3.6.6.1.5
_phasing_mir_der.der_set_id 3.6.6.1.5
_phasing_mir_der.native_set_id 3.6.6.1.5
PHASING_MIR_DER_REFLN 3.6.6.1, 3.6.6.1.5, 3.6.6.1.5
_phasing_mir_der_refln.der_id 3.6.6.1.5
_phasing_mir_der_refln.set_id 3.6.6.1.5
PHASING_MIR_DER_SHELL 3.6.6.1, 3.6.6.1, 3.6.6.1.5, 3.6.6.1.5
PHASING_MIR_DER_SITE 3.6.6.1, 3.6.6.1.5, 3.6.6.1.5
PHASING_MIR_SHELL 3.6.6.1.5, 3.6.6.1.5
_phasing_set_refln.set_id 3.6.6.1.6
Protein Data Bank 3.6.8
data exchange dictionary A3.6.2
Protein Data Bank Japan A3.6.2
Protein Expression Purification and Crystallization database (PEPCdb) A3.6.2.3.3
protein production A3.6.2.3.3
PROTIN/PROLSQ 3.6.6.2.3
_publ_section_references 3.6.8.1
_publ.section_references 3.6.8.1
PUBL_MANUSCRIPT_INCL 3.6.8.4, 3.6.8.4.2, 3.6.8.4.2
publishing
data items (mmCIF) 3.6.8
redundancy 3.6.6.2.1
_refine.correlation_coeff_Fo_to_Fc 3.6.6.2.1
_refine.details 3.6.6.2.1
_refine.entry_id 3.6.6.2.1
_refine.ls_percent_reflns_obs 3.6.6.2.1
_refine.ls_R_factor_obs 3.6.6.2.1, 3.6.6.2.1
_refine.ls_R_factor_R_work 3.6.6.2.1, 3.6.6.2.1
_refine.overall_SU_B 3.6.6.2.1
_refine.overall_SU_ML 3.6.6.2.1
_refine.overall_SU_R_Cruickshank_DPI 3.6.6.2.1
_refine.overall_SU_R_free 3.6.6.2.1
_refine_b_iso.class 3.6.6.2.4
REFINE_FUNCT_MINIMIZED 3.6.6.2, 3.6.6.2.1, 3.6.6.2.1, 3.6.6.2.1
_refine_ls_restr.type 3.6.6.2.3, 3.6.6.2.3
REFINE_LS_RESTR_NCS 3.6.6.2, 3.6.6.2.3, 3.6.6.2.3, 3.6.6.2.3
_refine_ls_restr_ncs.ncs_model_details 3.6.6.2.3
REFINE_LS_RESTR_TYPE 3.6.6.2, 3.6.6.2.3, 3.6.6.2.3, 3.6.6.2.3
_refine_occupancy.class 3.6.6.2.4
refinement
cycle 3.6.6.2.5
ideal groups 3.6.7.3
mmCIF data items 3.6.6.2, 3.6.6.2.5
quality metrics 3.6.6.2.2
restraints 3.6.6.2.3, 3.6.7.2.3
solvent (mmCIF) 3.6.6.2.1
_refln_sys_abs.I_over_sigmaI 3.6.6.3.1
_reflns.observed_criterion 3.6.6.3.2
_reflns.R_free_details 3.6.6.2.1
Research Collaboratory for Structural Bioinformatics A3.6.2
resolution limits 3.6.6.1.5
resolution shells 3.6.6.1.4, 3.6.6.1.5, 3.6.6.2.3, 3.6.6.2.3
RESTRAIN 3.6.6.2.3
R factor 3.6.6.2.1
Hamilton generalized 3.6.6.2.2
Luzzati analysis 3.6.6.2.2
real-space 3.6.7.5.4
Rmerge 3.6.6.3.2
secondary structure (protein) 3.6.7.5.2
sequence, macromolecular 3.6.7.1.1, 3.6.7.5.2
sequence alignment 3.6.7.5.6
sequence heterogeneity 3.6.3, 3.6.3, 3.6.7.3.2
_software.citation_id 3.6.8.2
_software.contact_author 3.6.8.2
_software.contact_author_email 3.6.8.2
_software.date 3.6.8.2
_software.location 3.6.8.2
_software.name 3.6.8.2
_software.version 3.6.8.2, 3.6.8.2
SPACE_GROUP 3.6.7.6, 3.6.7.6, 3.6.7.6
SPACE_GROUP_SYMOP 3.6.7.6, 3.6.7.6
standard uncertainty
overall measures (mmCIF) 3.6.6.2.1
separate data names (mmCIF) 3.6.4
_struct_biol.details 3.6.7.5.1
STRUCT_BIOL_KEYWORDS 3.6.7.5, 3.6.7.5.1, 3.6.7.5.1, 3.6.7.5.1, 3.6.7.8
STRUCT_BIOL_VIEW 3.6.7.5, 3.6.7.5.1, 3.6.7.5.1
_struct_biol_view.details 3.6.7.5.1
_struct_conf.details 3.6.7.5.2
_struct_conf_type.criteria 3.6.7.5.2
_struct_conf_type.id 3.6.7.5.2
_struct_conf_type.reference 3.6.7.5.2
_struct_conn.conn_type_id 3.6.7.5.3
_struct_conn.details 3.6.7.5.3
_struct_conn_type.criteria 3.6.7.5.3
_struct_conn_type.id 3.6.7.5.3
_struct_conn_type.reference 3.6.7.5.3
STRUCT_MON_DETAILS 3.6.7.5, 3.6.7.5.4, 3.6.7.5.4
_struct_mon_details.prot_cis 3.6.7.5.4
_struct_mon_details.RSR 3.6.7.5.4
STRUCT_MON_NUCL 3.6.7.5, 3.6.7.5.4, 3.6.7.5.4
STRUCT_MON_PROT 3.6.7.5, 3.6.7.5.4, 3.6.7.5.4
STRUCT_MON_PROT_CIS 3.6.7.5, 3.6.7.5.4, 3.6.7.5.4, 3.6.7.5.4
_struct_ncs_ens.id 3.6.7.5.5
_struct_ncs_oper.code 3.6.7.5.5, 3.6.7.5.5
_struct_ref.biol_id 3.6.7.5.6
_struct_ref.entity_id 3.6.7.5.6
_struct_ref.id 3.6.7.5.6
_struct_ref.seq_align 3.6.7.5.6
_struct_ref.seq_dif 3.6.7.5.6
_struct_ref_seq.details 3.6.7.5.6
STRUCT_REF_SEQ_DIF 3.6.7.5, 3.6.7.5.6, 3.6.7.5.6
_struct_ref_seq_dif.details 3.6.7.5.6
STRUCT_SHEET_* 3.6.7.5.2
_struct_sheet_range.symmetry 3.6.7.5.7
STRUCT_SHEET_TOPOLOGY 3.6.7.5, 3.6.7.5.7, 3.6.7.5.7, 3.6.7.5.7
_struct_site.details 3.6.7.5.8
_struct_site.id 3.6.7.5.8
_struct_site_gen.details 3.6.7.5.8
_struct_site_gen.symmetry 3.6.7.5.8
STRUCT_SITE_KEYWORDS 3.6.7.5, 3.6.7.5.1, 3.6.7.5.8, 3.6.7.5.8
STRUCT_SITE_VIEW 3.6.7.5, 3.6.7.5.8, 3.6.7.5.8, 3.6.7.5.8
_struct_site_view.details 3.6.7.5.8
structural genomics A3.6.2.2
structural model
mmCIF data items 3.6.7
Structural Proteomics in Europe A3.6.2.3.3
structure analysis
mmCIF 3.6.6
_symmetry.entry_id 3.6.7.6
SYMMETRY_EQUIV 3.6.7.6, 3.6.7.6, 3.6.7.6
symmetry
mmcif 3.6.7.6
systematic absences 3.6.6.3.1
torsion angle 3.6.7.2.2, 3.6.7.2.3, 3.6.7.5.4
unit cell
parameters and measurement conditions 3.6.5.1
VALENCE_PARAM 3.6.7.7, 3.6.7.7
VALENCE_REF 3.6.7.7, 3.6.7.7
visualization 3.6.3
web sites
PDB deposition: http://deposit.pdb.org/ A3.6.2.3.3
PDB mmCIF site: http://mmcif.pdb.org/ A3.6.2, A3.6.2.3.2
PDB Protein Expression Purification and Crystallization Database: http://pepcdb.pdb.org/ A3.6.2.3.3
PDB software tools: http://sw-tools.pdb.org/ A3.6.2.4
Structural Proteomics in Europe: http://www.spineurope.org/ A3.6.2.3.3
Wilson B factor 3.6.6.3.2
Worldwide PDB A3.6.2