International Tables for Crystallography (2006). Vol. F. ch. 18.4, pp. 393-402   | 1 | 2 |
https://doi.org/10.1107/97809553602060000696

Chapter 18.4. Refinement at atomic resolution

Contents

  • 18.4. Refinement at atomic resolution  (pp. 393-402) | html | pdf | chapter contents |
    Z. Dauter, G. N. Murshudov and K. S. Wilson
    • 18.4.1. Definition of atomic resolution  (pp. 393-395) | html | pdf |
      • 18.4.1.1. Ab initio phasing and atomic resolution  (p. 395) | html | pdf |
    • 18.4.2. Data  (p. 395) | html | pdf |
      • 18.4.2.1. Data quality  (p. 395) | html | pdf |
      • 18.4.2.2. Anisotropic scaling  (p. 395) | html | pdf |
    • 18.4.3. Computational algorithms and strategies  (p. 396) | html | pdf |
      • 18.4.3.1. Classical least-squares refinement of small molecules  (p. 396) | html | pdf |
      • 18.4.3.2. Least-squares refinement of large structures  (p. 396) | html | pdf |
      • 18.4.3.3. Fast Fourier transform  (p. 396) | html | pdf |
      • 18.4.3.4. Maximum likelihood  (p. 396) | html | pdf |
      • 18.4.3.5. Computer power  (p. 396) | html | pdf |
    • 18.4.4. Computational options and tactics  (pp. 396-398) | html | pdf |
      • 18.4.4.1. Use of F or F2  (pp. 396-397) | html | pdf |
      • 18.4.4.2. Restraints and/or constraints on coordinates and ADPs  (p. 397) | html | pdf |
      • 18.4.4.3. Partial occupancy  (p. 397) | html | pdf |
      • 18.4.4.4. Validation of extra parameters during the refinement process  (pp. 397-398) | html | pdf |
      • 18.4.4.5. Practical strategies  (p. 398) | html | pdf |
    • 18.4.5. Features in the refined model  (pp. 398-401) | html | pdf |
      • 18.4.5.1. Hydrogen atoms  (pp. 398-399) | html | pdf |
      • 18.4.5.2. Anisotropic atomic displacement parameters  (p. 399) | html | pdf |
      • 18.4.5.3. Alternative conformations  (p. 399) | html | pdf |
      • 18.4.5.4. Ordered solvent water  (pp. 399-400) | html | pdf |
      • 18.4.5.5. Automatic location of water sites  (p. 400) | html | pdf |
      • 18.4.5.6. Bulk solvent and the low-resolution reflections  (pp. 400-401) | html | pdf |
      • 18.4.5.7. Metal ions and other ligands in the solvent  (p. 401) | html | pdf |
      • 18.4.5.8. Deformation density  (p. 401) | html | pdf |
    • 18.4.6. Quality assessment of the model  (p. 401) | html | pdf |
    • 18.4.7. Relation to biological chemistry   (pp. 401-402) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 18.4.1.1. The thermal-ellipsoid model used to represent anisotropic atomic displacement, with major axes indicated  (p. 393) | html | pdf |
      • Fig. 18.4.1.2. Histograms of B values for a protein structure, Micrococcus lysodecticus catalase (Murshudov et al  (p. 394) | html | pdf |
      • Fig. 18.4.5.1. (a), (b) Representative electron-density maps for the refinement of Clostridium acidurici ferredoxin at 0.94 Å resolution (Dauter, Wilson et al  (p. 398) | html | pdf |
      • Fig. 18.4.5.2. Schematic representation of the bulk-solvent models described in the text  (p. 400) | html | pdf |
    • Tables
      • Table 18.4.1.1. The parameters of an atomic model  (p. 393) | html | pdf |
      • Table 18.4.1.2. Features which can be seen in the electron density at different resolutions  (p. 394) | html | pdf |