International Tables for Crystallography (2012). Vol. F. ch. 21.2, pp. 662-676   | 1 | 2 |
https://doi.org/10.1107/97809553602060000880

Chapter 21.2. Assessing the quality of macromolecular structures

Contents

  • 21.2. Assessing the quality of macromolecular structures  (pp. 662-676) | html | pdf | chapter contents |
    S. J. Wodak, A. A. Vagin, J. Richelle, U. Das, J. Pontius and H. M. Berman
    • 21.2.1. Introduction  (p. 662) | html | pdf |
    • 21.2.2. Validating the geometric and stereochemical parameters of the model  (pp. 662-665) | html | pdf |
      • 21.2.2.1. Comparisons against standard values derived from crystals of small molecules  (pp. 662-663) | html | pdf |
      • 21.2.2.2. Comparisons against standard values derived from surveys of other macromolecules  (pp. 663-665) | html | pdf |
        • 21.2.2.2.1. Validation of stereochemical and non-bonded parameters   (p. 663) | html | pdf |
        • 21.2.2.2.2. Validation using knowledge-based interaction potentials and profiles  (pp. 663-664) | html | pdf |
        • 21.2.2.2.3. Deviations from standard atomic volumes as a quality measure for protein crystal structures  (pp. 664-665) | html | pdf |
    • 21.2.3. Validation of a model versus experimental data  (pp. 665-673) | html | pdf |
      • 21.2.3.1. A systematic approach using the SFCHECK software  (pp. 666-673) | html | pdf |
        • 21.2.3.1.1. Tasks performed by SFCHECK  (pp. 666-667) | html | pdf |
          • 21.2.3.1.1.1. Treatment of structure-factor data and scaling  (p. 666) | html | pdf |
          • 21.2.3.1.1.2. Global agreement between the model and experimental data  (p. 666) | html | pdf |
          • 21.2.3.1.1.3. Estimations of errors in atomic positions  (p. 667) | html | pdf |
          • 21.2.3.1.1.4. Local agreement between the model and the experimental data  (p. 667) | html | pdf |
        • 21.2.3.1.2. Evaluation of individual structures  (pp. 667-668) | html | pdf |
        • 21.2.3.1.3. Quality assessment based on surveys across structures  (pp. 668-673) | html | pdf |
          • 21.2.3.1.3.1. Assessing the quality of a structure as a whole  (pp. 668-669) | html | pdf |
          • 21.2.3.1.3.2. Assessing the quality in specific regions of a model  (pp. 670-673) | html | pdf |
    • 21.2.4. Atomic resolution structures  (p. 673) | html | pdf |
    • 21.2.5. Concluding remarks  (p. 673) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 21.2.2.1. The Voronoi polyhedron  (p. 664) | html | pdf |
      • Fig. 21.2.2.2. Atomic volume Z score r.m.s. variation with nominal resolution (d spacing) in 900 protein structures from the PDB  (p. 665) | html | pdf |
      • Fig. 21.2.3.1. Typical SFCHECK output in PostScript format, illustrated for the protein rusticyanin from Thiobacillus ferrooxidans (1RCY) (Walter et al., 1996)  (p. 668) | html | pdf |
      • Fig. 21.2.3.2. Graphical output from the SFCHECK analysis of global characteristics of the structure-factor data and the model agreement with those data for the same structure as in Fig. 21.2.3.1  (p. 669) | html | pdf |
      • Fig. 21.2.3.3. SFCHECK evaluation summary of the local agreement between the model and the electron density for the same structure as in Fig. 21.2.3.1  (pp. 671-672) | html | pdf |
      • Fig. 21.2.3.4. Variation of global quality indicators with the nominal resolution (d spacing) of the crystallographic data  (p. 672) | html | pdf |
      • Fig. 21.2.3.5. Pairwise correlations between the various local quality indicators computed by SFCHECK  (p. 673) | html | pdf |
      • Fig. 21.2.3.6. B factors and density indices for residues across different structures  (p. 674) | html | pdf |
    • Tables
      • Table 21.2.3.1. Parameters computed for the analysis of the structure-factor data  (p. 666) | html | pdf |
      • Table 21.2.3.2. Estimation of errors in atomic coordinates  (p. 667) | html | pdf |
      • Table 21.2.3.3. Parameters computed by SFCHECK to assess the quality of the model in specific regions  (p. 672) | html | pdf |