International Tables for Crystallography (2012). Vol. F, ch. 22.5, pp. 736-748   | 1 | 2 |
doi: 10.1107/97809553602060000889

Chapter 22.5. The relevance of the Cambridge Structural Database in protein crystallography

Contents

  • 22.5. The relevance of the Cambridge Structural Database in protein crystallography  (pp. 736-748) | html | pdf | chapter contents |
    • 22.5.1. Introduction  (p. 736) | html | pdf |
    • 22.5.2. The CSD and the PDB: data acquisition and data quality  (pp. 736-737) | html | pdf |
      • 22.5.2.1. Statistical inferences  (p. 736) | html | pdf |
      • 22.5.2.2. Data acquisition and completeness  (p. 737) | html | pdf |
      • 22.5.2.3. Standard formats: CIF and mmCIF  (p. 737) | html | pdf |
      • 22.5.2.4. Structure validation  (p. 737) | html | pdf |
    • 22.5.3. Structural knowledge from the CSD  (pp. 737-738) | html | pdf |
      • 22.5.3.1. The CSD software system  (p. 737) | html | pdf |
      • 22.5.3.2. CSD structures and substructures of relevance to protein studies  (p. 737) | html | pdf |
      • 22.5.3.3. Geometrical parameters of relevance to protein studies  (pp. 737-738) | html | pdf |
    • 22.5.4. Intramolecular geometry  (pp. 738-740) | html | pdf |
      • 22.5.4.1. Mean molecular dimensions  (pp. 738-739) | html | pdf |
      • 22.5.4.2. Conformational information  (p. 739) | html | pdf |
      • 22.5.4.3. Crystallographic conformations and energies  (pp. 739-740) | html | pdf |
      • 22.5.4.4. Conformational libraries  (p. 740) | html | pdf |
      • 22.5.4.5. Metal coordination geometry  (p. 740) | html | pdf |
    • 22.5.5. Intermolecular data  (pp. 740-745) | html | pdf |
      • 22.5.5.1. van der Waals radii  (p. 740) | html | pdf |
      • 22.5.5.2. Hydrogen-bond geometry and directionality  (pp. 740-741) | html | pdf |
      • 22.5.5.3. C—H··· X hydrogen bonds  (pp. 741-742) | html | pdf |
      • 22.5.5.4. O—H···π and N—H···π hydrogen bonds  (p. 742) | html | pdf |
      • 22.5.5.5. Other non-covalent interactions  (p. 742) | html | pdf |
      • 22.5.5.6. Intermolecular motif formation in small-molecule crystal structures  (pp. 742-743) | html | pdf |
      • 22.5.5.7. The answer `no'  (p. 743) | html | pdf |
      • 22.5.5.8. IsoStar: a library of non-bonded interactions  (p. 743) | html | pdf |
      • 22.5.5.9. Protein–ligand binding  (pp. 743-745) | html | pdf |
      • 22.5.5.10. Modelling applications that use CSD data  (p. 745) | html | pdf |
    • 22.5.6. Conclusion  (p. 745) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 22.5.2.1. ( a ) Growth rate of the CSD and ( b ) growth rate of the PDB, in terms of the numbers of structures published per annum for the period 1970–1995  (p. 736) | html | pdf |
      • Fig. 22.5.4.1. Distribution of torsion angles in C( sp 3 )—S—S—C( sp 3 ) substructures located in the CSD  (p. 739) | html | pdf |
      • Fig. 22.5.5.1. The IsoStar knowledge-based library of intermolecular interactions: interaction of O—H donors (contact groups) with one of the >C=O acceptors of a carboxylate group (the central group)  (p. 741) | html | pdf |
      • Fig. 22.5.5.2. Distribution of O—H donors around ether oxygen acceptors (CSD data from the IsoStar library, see text)  (p. 741) | html | pdf |
      • Fig. 22.5.5.3. Distribution of oxygen atoms around C(aromatic)—I (CSD data from the IsoStar library, see text)  (p. 743) | html | pdf |
      • Fig. 22.5.5.4. Pairwise comparison of intermolecular-interaction density maps from the CSD and the PDB  (p. 744) | html | pdf |
    • Tables
      • Table 22.5.3.1. Summary of amino-acid and peptide structures available in the CSD (April 1998, 181 309 entries)  (p. 738) | html | pdf |
      • Table 22.5.3.2. CSD entry statistics for selected metal-containing structures  (p. 738) | html | pdf |
      • Table 22.5.5.1. Residual densities for carboxylic acid groups  (p. 745) | html | pdf |