International Tables for Crystallography (2006). Vol. F. ch. 22.4, pp. 558-574   | 1 | 2 |
https://doi.org/10.1107/97809553602060000713

Chapter 22.4. The relevance of the Cambridge Structural Database in protein crystallography

Contents

  • 22.4. The relevance of the Cambridge Structural Database in protein crystallography  (pp. 558-574) | html | pdf | chapter contents |
    F. H. Allen, J. C. Cole and M. L. Verdonk
    • 22.4.1. Introduction  (p. 558) | html | pdf |
    • 22.4.2. The CSD and the PDB: data acquisition and data quality  (pp. 558-559) | html | pdf |
      • 22.4.2.1. Statistical inferences  (p. 558) | html | pdf |
      • 22.4.2.2. Data acquisition and completeness   (pp. 558-559) | html | pdf |
      • 22.4.2.3. Standard formats: CIF and mmCIF  (p. 559) | html | pdf |
      • 22.4.2.4. Structure validation  (p. 559) | html | pdf |
    • 22.4.3. Structural knowledge from the CSD  (pp. 559-560) | html | pdf |
      • 22.4.3.1. The CSD software system  (p. 559) | html | pdf |
      • 22.4.3.2. CSD structures and substructures of relevance to protein studies  (pp. 559-560) | html | pdf |
      • 22.4.3.3. Geometrical parameters of relevance to protein studies  (p. 560) | html | pdf |
    • 22.4.4. Intramolecular geometry  (pp. 560-562) | html | pdf |
      • 22.4.4.1. Mean molecular dimensions  (p. 560) | html | pdf |
      • 22.4.4.2. Conformational information  (pp. 560-561) | html | pdf |
      • 22.4.4.3. Crystallographic conformations and energies  (p. 561) | html | pdf |
      • 22.4.4.4. Conformational libraries  (pp. 561-562) | html | pdf |
      • 22.4.4.5. Metal coordination geometry  (p. 562) | html | pdf |
    • 22.4.5. Intermolecular data  (pp. 562-567) | html | pdf |
      • 22.4.5.1. van der Waals radii  (p. 562) | html | pdf |
      • 22.4.5.2. Hydrogen-bond geometry and directionality  (p. 562) | html | pdf |
      • 22.4.5.3. C—H···X hydrogen bonds  (p. 563) | html | pdf |
      • 22.4.5.4. O—H···π and N—H···π hydrogen bonds  (pp. 563-564) | html | pdf |
      • 22.4.5.5. Other non-covalent interactions  (p. 564) | html | pdf |
      • 22.4.5.6. Intermolecular motif formation in small-molecule crystal structures  (p. 564) | html | pdf |
      • 22.4.5.7. The answer `no'  (pp. 564-565) | html | pdf |
      • 22.4.5.8. IsoStar: a library of non-bonded interactions   (p. 565) | html | pdf |
      • 22.4.5.9. Protein–ligand binding  (pp. 565-566) | html | pdf |
      • 22.4.5.10. Modelling applications that use CSD data  (pp. 566-567) | html | pdf |
    • 22.4.6. Conclusion  (p. 567) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 22.4.2.1. (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. 558) | html | pdf |
      • Fig. 22.4.4.1. Distribution of torsion angles in C(sp3)—S—S—C(sp3) substructures located in the CSD  (p. 561) | html | pdf |
      • Fig. 22.4.5.1. 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. 563) | html | pdf |
      • Fig. 22.4.5.2. Distribution of O—H donors around ether oxygen acceptors (CSD data from the IsoStar library, see text)  (p. 563) | html | pdf |
      • Fig. 22.4.5.3. Distribution of oxygen atoms around C(aromatic)—I (CSD data from the IsoStar library, see text)  (p. 564) | html | pdf |
      • Fig. 22.4.5.4. Pairwise comparison of intermolecular-interaction density maps from the CSD and the PDB  (p. 566) | html | pdf |
    • Tables
      • Table 22.4.3.1. Summary of amino-acid and peptide structures available in the CSD (April 1998, 181 309 entries)  (p. 559) | html | pdf |
      • Table 22.4.3.2. CSD entry statistics for selected metal-containing structures  (p. 560) | html | pdf |
      • Table 22.4.5.1. Residual densities for carboxylic acid groups  (p. 566) | html | pdf |