Crystallographic model quality at a glance

Acta Crystallogr D Biol Crystallogr. 2009 Mar;65(Pt 3):297-300. doi: 10.1107/S0907444908044296. Epub 2009 Feb 20.

Abstract

A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from ;ideal values' is shown graphically as a point on a ;ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in ;red zones' indicate parameters which lie outside typical values.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Computer Graphics*
  • Crystallography, X-Ray* / statistics & numerical data
  • Macromolecular Substances / chemistry*
  • Models, Molecular*
  • Molecular Conformation*
  • Stereoisomerism
  • Validation Studies as Topic*

Substances

  • Macromolecular Substances