InternationalCrystallography of biological macromoleculesTables for Crystallography Volume F Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 21.1, pp. 498-499
## Section 21.1.3.2. Local statistics |

From a practical point of view, these are the most useful for the crystallographer who is about to rebuild a model. Examples of useful quality indicators are:

In addition to these criteria, residues with other unusual features should be examined in the electron-density maps for the crystallographer to be able to decide whether they are in error. Such features may pertain to unusual temperature factors, unusual occupancies, unusual bond lengths or angles, unusual torsion angles or deviations from planarity (*e.g.* for the peptide plane), unusual chirality (*e.g.* for the C^{α} atom of every residue type except glycine), unusual differences in the temperature factors of chemically bonded atoms, unusual packing environments (Vriend & Sander, 1993), very short distances between non-bonded atoms (including symmetry mates), large positional shifts during refinement, unusual deviations from noncrystallographic symmetry (Kleywegt & Jones, 1995*b*; Kleywegt, 1996) *etc.*

### References

Bhat, T. N. & Cohen, G. H. (1984).*OMITMAP: an electron density map suitable for the examination of errors in a macromolecular model.*

*J. Appl. Cryst.*

**17**, 244–248.Google Scholar

Chapman, M. S. (1995).

*Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function.*

*Acta Cryst.*A

**51**, 69–80.Google Scholar

Hodel, A., Kim, S.-H. & Brünger, A. T. (1992).

*Model bias in macromolecular crystal structures.*

*Acta Cryst.*A

**48**, 851–858.Google Scholar

Hooft, R. W. W., Sander, C. & Vriend, G. (1996

*b*).

*Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures.*

*Proteins Struct. Funct. Genet.*

**26**, 363–376.Google Scholar

Jones, T. A. & Kjeldgaard, M. (1997).

*Electron density map interpretation.*

*Methods Enzymol.*

**277**, 173–208.Google Scholar

Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991).

*Improved methods for building protein models in electron density maps and the location of errors in these models.*

*Acta Cryst.*A

**47**, 110–119.Google Scholar

Kleywegt, G. J. (1996).

*Use of non-crystallographic symmetry in protein structure refinement.*

*Acta Cryst.*D

**52**, 842–857.Google Scholar

Kleywegt, G. J. & Jones, T. A. (1995

*b*).

*Where freedom is given, liberties are taken.*

*Structure*,

**3**, 535–540.Google Scholar

Kleywegt, G. J. & Jones, T. A. (1996

*b*).

*Phi/Psi-chology: Ramachandran revisited.*

*Structure*,

**4**, 1395–1400.Google Scholar

Kleywegt, G. J. & Jones, T. A. (1997).

*Model-building and refinement practice.*

*Methods Enzymol.*

**277**, 208–230.Google Scholar

Kleywegt, G. J. & Jones, T. A. (1998).

*Databases in protein crystallography.*

*Acta Cryst.*D

**54**, 1119–1131.Google Scholar

Kleywegt, G. J. & Read, R. J. (1997).

*Not your average density.*

*Structure*,

**5**, 1557–1569.Google Scholar

Ramakrishnan, C. & Ramachandran, G. N. (1965).

*Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units.*

*Biophys. J.*

**5**, 909–933.Google Scholar

Read, R. J. (1986).

*Improved Fourier coefficients for maps using phases from partial structures with errors.*

*Acta Cryst.*A

**42**, 140–149.Google Scholar

Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999).

*SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.*

*Acta Cryst.*D

**55**, 191–205.Google Scholar

Vriend, G. & Sander, C. (1993).

*Quality control of protein models: directional atomic contact analysis.*

*J. Appl. Cryst.*

**26**, 47–60.Google Scholar

Zou, J. Y. & Mowbray, S. L. (1994).

*An evaluation of the use of databases in protein structure refinement.*

*Acta Cryst.*D

**50**, 237–249.Google Scholar