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

Contents

  • 3.6. Classification and use of macromolecular data  (pp. 144-198) | html | pdf | chapter contents |
    P. M. D. Fitzgerald, J. D. Westbrook, P. E. Bourne, B. McMahon, K. D. Watenpaugh and H. M. Berman
    • 3.6.1. Introduction  (p. 144) | html | pdf |
    • 3.6.2. Considerations underlying the design of the dictionary  (pp. 144-145) | html | pdf |
    • 3.6.3. Overview of the mmCIF data model  (pp. 145-147) | html | pdf |
    • 3.6.4. Content of the macromolecular CIF dictionary  (pp. 147-148) | html | pdf |
    • 3.6.5. Experimental measurements  (pp. 148-152) | html | pdf |
      • 3.6.5.1. Crystal cell parameters and measurement conditions  (pp. 148-149) | html | pdf |
      • 3.6.5.2. Data collection  (pp. 149-151) | html | pdf |
      • 3.6.5.3. Growth, description and analysis of the crystal  (pp. 151-152) | html | pdf |
        • 3.6.5.3.1. Crystal properties  (pp. 151-152) | html | pdf |
        • 3.6.5.3.2. Crystal growth  (p. 152) | html | pdf |
    • 3.6.6. Analysis  (pp. 152-164) | html | pdf |
      • 3.6.6.1. Phasing  (pp. 152-158) | html | pdf |
        • 3.6.6.1.1. Overall description of phasing  (p. 153) | html | pdf |
        • 3.6.6.1.2. Phasing via molecular averaging  (p. 153) | html | pdf |
        • 3.6.6.1.3. Phasing via isomorphous replacement  (pp. 153-154) | html | pdf |
        • 3.6.6.1.4. Phasing via multiple-wavelength anomalous dispersion  (pp. 154-155) | html | pdf |
        • 3.6.6.1.5. Phasing via multiple isomorphous replacement  (pp. 155-157) | html | pdf |
        • 3.6.6.1.6. Phasing data sets  (pp. 157-158) | html | pdf |
      • 3.6.6.2. Refinement  (pp. 158-162) | html | pdf |
        • 3.6.6.2.1. Overall description of the refinement  (pp. 158-159) | html | pdf |
        • 3.6.6.2.2. Analysis of the refined structure  (pp. 159-160) | html | pdf |
        • 3.6.6.2.3. Restraints and refinement by shells of resolution  (pp. 160-161) | html | pdf |
        • 3.6.6.2.4. Equivalent atoms in the refinement  (pp. 161-162) | html | pdf |
        • 3.6.6.2.5. History of the refinement  (p. 162) | html | pdf |
      • 3.6.6.3. Reflection measurements  (pp. 162-164) | html | pdf |
        • 3.6.6.3.1. Individual reflections  (pp. 162-163) | html | pdf |
        • 3.6.6.3.2. Groups of reflections  (pp. 163-164) | html | pdf |
    • 3.6.7. Atomicity, chemistry and structure  (pp. 164-190) | html | pdf |
      • 3.6.7.1. Atom sites  (pp. 164-169) | html | pdf |
        • 3.6.7.1.1. Individual atom sites  (pp. 164-166) | html | pdf |
        • 3.6.7.1.2. Collections of atom sites  (p. 167) | html | pdf |
        • 3.6.7.1.3. Atom types  (p. 167) | html | pdf |
        • 3.6.7.1.4. Alternative conformations  (pp. 168-169) | html | pdf |
      • 3.6.7.2. Molecular chemistry  (pp. 169-174) | html | pdf |
        • 3.6.7.2.1. Molecular chemistry in the core CIF dictionary  (p. 169) | html | pdf |
        • 3.6.7.2.2. Chemical components  (pp. 169-172) | html | pdf |
        • 3.6.7.2.3. Chemical links  (pp. 172-174) | html | pdf |
      • 3.6.7.3. Distinct chemical species  (pp. 174-176) | html | pdf |
        • 3.6.7.3.1. Description of entities  (pp. 174-175) | html | pdf |
        • 3.6.7.3.2. Polymer entities  (pp. 175-176) | html | pdf |
      • 3.6.7.4. Molecular or packing geometry  (pp. 176-178) | html | pdf |
      • 3.6.7.5. Molecular structure  (pp. 178-189) | html | pdf |
        • 3.6.7.5.1. Higher-level macromolecular structure  (pp. 179-181) | html | pdf |
        • 3.6.7.5.2. Secondary structure  (pp. 181-182) | html | pdf |
        • 3.6.7.5.3. Structural interactions  (pp. 182-183) | html | pdf |
        • 3.6.7.5.4. Structural features of monomers  (pp. 183-184) | html | pdf |
        • 3.6.7.5.5. Noncrystallographic symmetry  (pp. 184-186) | html | pdf |
        • 3.6.7.5.6. External databases  (pp. 186-187) | html | pdf |
        • 3.6.7.5.7. β-sheets  (pp. 187-188) | html | pdf |
        • 3.6.7.5.8. Molecular sites  (pp. 188-189) | html | pdf |
      • 3.6.7.6. Crystal symmetry  (p. 190) | html | pdf |
      • 3.6.7.7. Bond-valence information  (p. 190) | html | pdf |
    • 3.6.8. Publication  (pp. 190-194) | html | pdf |
      • 3.6.8.1. Literature citations  (pp. 190-191) | html | pdf |
      • 3.6.8.2. Citation of software packages  (p. 191) | html | pdf |
      • 3.6.8.3. Citation of related database entries  (pp. 191-193) | html | pdf |
        • 3.6.8.3.1. Related database entries  (p. 192) | html | pdf |
        • 3.6.8.3.2. Compatibility with PDB format files  (pp. 192-193) | html | pdf |
      • 3.6.8.4. Article publication  (pp. 193-194) | html | pdf |
        • 3.6.8.4.1. Journal housekeeping and citation entries  (pp. 193-194) | html | pdf |
        • 3.6.8.4.2. Contents of a publication  (p. 194) | html | pdf |
    • 3.6.9. File metadata  (pp. 194-195) | html | pdf |
      • 3.6.9.1. History of a data block  (p. 194) | html | pdf |
      • 3.6.9.2. Links between data blocks  (pp. 194-195) | html | pdf |
      • 3.6.9.3. Other category classifications  (p. 195) | html | pdf |
    • Appendix 3.6.1. Category structure of the mmCIF dictionary  (p. 195) | html | pdf |
    • Appendix 3.6.2. The Protein Data Bank exchange data dictionary  (pp. 195-197) | html | pdf |
      J. D. Westbrook, K. Henrick, E. L. Ulrich and H. M. Berman
      • A3.6.2.1. Data exchange and format translation   (pp. 195-196) | html | pdf |
      • A3.6.2.2. Extensions for structural genomics  (p. 197) | html | pdf |
      • A3.6.2.3. Noncrystallographic methods  (p. 197) | html | pdf |
        • A3.6.2.3.1. NMR  (p. 197) | html | pdf |
        • A3.6.2.3.2. Cryo-electron microscopy  (p. 197) | html | pdf |
        • A3.6.2.3.3. Protein production  (p. 197) | html | pdf |
      • A3.6.2.4. Supporting software  (p. 197) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 3.6.3.1. A representation of crambin (PDB 3CNR) with a co-crystallized ethanol molecule  (p. 145) | html | pdf |
      • Fig. 3.6.6.1. The family of categories used to describe MAD phasing  (p. 155) | html | pdf |
      • Fig. 3.6.6.2. The family of categories used to describe MIR phasing  (p. 156) | html | pdf |
      • Fig. 3.6.7.1. The family of categories used to describe atom sites  (p. 165) | html | pdf |
      • Fig. 3.6.7.2. Alternative conformations in an HIV-1 protease structure (PDB 5HVP) to be described with data items in the ATOM_SITES_ALT, ATOM_SITES_ALT_ENS and ATOM_SITES_ALT_GEN categories  (p. 168) | html | pdf |
      • Fig. 3.6.7.3. The family of categories used to describe the chemical and structural features of the monomers and small molecules used to build a model of a structure  (p. 171) | html | pdf |
      • Fig. 3.6.7.4. The family of categories used to describe the links between chemical components  (p. 173) | html | pdf |
      • Fig. 3.6.7.5. The family of categories used to describe chemical entities  (p. 175) | html | pdf |
      • Fig. 3.6.7.6. The family of categories used to describe polymer chemical entities  (p. 176) | html | pdf |
      • Fig. 3.6.7.7. The family of categories used to describe the higher-level macromolecular structure  (p. 179) | html | pdf |
      • Fig. 3.6.7.8. The higher-level structure of the complex of HIV-1 protease with an inhibitor (PDB 5HVP) to be described with data items in the STRUCT_ASYM, STRUCT_BIOL, STRUCT_BIOL_KEYWORDS and STRUCT_BIOL_GEN categories  (p. 180) | html | pdf |
      • Fig. 3.6.7.9. The family of categories used to describe secondary structure  (p. 181) | html | pdf |
      • Fig. 3.6.7.10. The family of categories used to describe structural interactions such as hydrogen bonding, salt bridges and disulfide bridges  (p. 182) | html | pdf |
      • Fig. 3.6.7.11. The family of categories used to describe the structural features of monomers  (p. 184) | html | pdf |
      • Fig. 3.6.7.12. The family of categories used to describe noncrystallographic symmetry  (p. 185) | html | pdf |
      • Fig. 3.6.7.13. Noncrystallographic symmetry in the structure of trimeric haemerythrin (PDB 1HR3) to be described with data items in the STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, STRUCT_NCS_DOM and STRUCT_NCS_DOM_LIM categories  (p. 185) | html | pdf |
      • Fig. 3.6.7.14. The family of categories used to describe β-sheets  (p. 188) | html | pdf |
      • Fig. 3.6.7.15. A hypothetical β-sheet to be described with data items in the STRUCT_SHEET, STRUCT_SHEET_ORDER, STRUCT_SHEET_RANGE and STRUCT_SHEET_HBOND categories  (p. 188) | html | pdf |
      • Fig. 3.6.7.16. The family of categories used to describe molecular sites  (p. 189) | html | pdf |
    • Tables
      • Table 3.6.4.1. Major category groups defined in the mmCIF dictionary  (p. 148) | html | pdf |
      • Table A3.6.1.1. Categories in the mmCIF dictionary  (p. 196) | html | pdf |