Bias in cross-validated free R factors: Mitigation of the effects of non-crystallographic symmetry

Felcy Fabiola, Andrei Korostelev, Michael Chapman

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Current methods of free R factor cross-validation assume that the structure factors of the test and working sets are independent of one another. This assumption is only an approximation when the modeled structure occupies anything less than the full asymmetric unit. Through progressive elimination of reflections from the working set, starting with those expected to be most correlated to the test set, small biases in free R can be measured, presumably because of over-sampling of the Fourier transform owing to bulk solvent in the crystal. This level of bias may be of little practical importance, but it rises to significant levels with increasing non-crystallographic symmetry owing to wider correlations between structure factors than hitherto appreciated. In the presence of 15-fold non-crystallographic symmetry, with resolutions commonly attainable in macromolecular crystallography, it may not be possible to calculate an unbiased free R factor. Methods are developed for the calculation of reduced-bias free R factors through elimination of the strongest correlations between test and working sets. With 180-fold non-crystallographic symmetry they may not be an accurate indicator of absolute quality, but they do yield the correct optimal weighting for stereochemical restraints.

Original languageEnglish (US)
Pages (from-to)227-238
Number of pages12
JournalActa Crystallographica Section D: Biological Crystallography
Volume62
Issue number3
DOIs
StatePublished - Mar 2006
Externally publishedYes

Fingerprint

R Factors
R388
Crystallography
symmetry
Fourier Analysis
Crystal symmetry
elimination
Fourier transforms
Sampling
Crystals
crystallography
sampling
approximation
crystals

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics
  • Condensed Matter Physics
  • Structural Biology

Cite this

Bias in cross-validated free R factors : Mitigation of the effects of non-crystallographic symmetry. / Fabiola, Felcy; Korostelev, Andrei; Chapman, Michael.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 62, No. 3, 03.2006, p. 227-238.

Research output: Contribution to journalArticle

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