International Tables for Crystallography (2012). Vol. F. ch. 18.3, pp. 474-484   | 1 | 2 |
https://doi.org/10.1107/97809553602060000857

Chapter 18.3. Structure quality and target parameters

Contents

  • 18.3. Structure quality and target parameters  (pp. 474-484) | html | pdf | chapter contents |
    R. A. Engh and R. Huber
    • 18.3.1. Purpose of restraints  (p. 474) | html | pdf |
      • 18.3.1.1. Utility of restraints: protein/special geometries  (p. 474) | html | pdf |
      • 18.3.1.2. Risk of restraints: bias, lack of cross validation  (p. 474) | html | pdf |
    • 18.3.2. Formulation of refinement restraints  (pp. 475-483) | html | pdf |
      • 18.3.2.1. Choice of properties for restraint  (p. 475) | html | pdf |
      • 18.3.2.2. Simple derivation of force constants from parameter distributions  (pp. 475-477) | html | pdf |
        • 18.3.2.2.1. Clustering  (pp. 475-477) | html | pdf |
        • 18.3.2.2.2. Treatment of outliers  (p. 477) | html | pdf |
      • 18.3.2.3. Bonds and angles  (pp. 477-481) | html | pdf |
        • 18.3.2.3.1. Peptide parameters: proline, glycine, alanine and CB substitution  (pp. 477-478) | html | pdf |
        • 18.3.2.3.2. Aromatic residues: tryptophan, phenylalanine, tyrosine, histidine  (pp. 480-481) | html | pdf |
        • 18.3.2.3.3. Aliphatic residues: leucine, isoleucine, valine  (p. 481) | html | pdf |
        • 18.3.2.3.4. Neutral polar residues: serine, threonine, glutamine, asparagine  (p. 481) | html | pdf |
        • 18.3.2.3.5. Acidic residues: glutamate, aspartate  (p. 481) | html | pdf |
        • 18.3.2.3.6. Basic residues: arginine, lysine  (p. 481) | html | pdf |
        • 18.3.2.3.7. Sulfur-containing residues: methionine, cysteine, disulfides  (p. 481) | html | pdf |
      • 18.3.2.4. Planarity restraints  (pp. 481-482) | html | pdf |
      • 18.3.2.5. Torsion angles  (p. 482) | html | pdf |
      • 18.3.2.6. Non-bonded interactions  (p. 482) | html | pdf |
      • 18.3.2.7. Effects of hydrogen atoms in parameterization  (p. 482) | html | pdf |
      • 18.3.2.8. Special geometries: cofactors, ligands, metals etc.  (pp. 482-483) | html | pdf |
      • 18.3.2.9. Addition of tailored information sources  (p. 483) | html | pdf |
    • 18.3.3. Strategy of application during building/refinement  (p. 483) | html | pdf |
      • 18.3.3.1. Confidence in restraints versus information from diffraction  (p. 483) | html | pdf |
    • 18.3.4. Future perspectives  (p. 483) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 18.3.2.1. Torsion dependence of proline angle geometry  (p. 478) | html | pdf |
      • Fig. 18.3.2.2. Bimodal distributions for tyrosine  (p. 478) | html | pdf |
      • Fig. 18.3.2.3. Tryptophan [\chi_{2}] dihedral angle distribution  (p. 481) | html | pdf |
    • Tables
      • Table 18.3.2.1. Bond lengths of standard amino-acid side chains  (pp. 476-477) | html | pdf |
      • Table 18.3.2.2. Bond angles of standard amino-acid side chains  (pp. 479-480) | html | pdf |
      • Table 18.3.2.3. Bond lengths (Å) and angles (°) of peptide backbone fragments  (p. 482) | html | pdf |