In some of the cases discussed in the thread, a less biased Rfree could be
calculated by procedures discussed in the paper below. Felcy, a post-doc of
mine, followed ideas discussed by several at conferences and examined
systematically the impact of NCS on Rfree, and how to mitigate the effect.
She put together procedures that excluded correlated reflections that I
think would eliminate the challenges of cross-validation in the pathological
cases. (I also think that her discussion will address some of the concerns
in the thread about the independence of reflections etc.).
Michael.
Fabiola, F., A. Korostelev, et al. (2006). "Bias in cross-validated free R
factors: mitigation of the effects of non-crystallographic symmetry." Acta
Crystallogr D Biol Crystallogr 62(Pt 3): 227-38.
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.
Michael S. Chapman, R.T. Jones Professor of Structural Biology
Dept. Biochemistry & Molecular Biology; School of Medicine, Mail Code L224
Oregon Health & Science University
3181 Sam Jackson Park Road; Portland, OR 97239-3098
[EMAIL PROTECTED] / (503) 494-1025; http://xtal.ohsu.edu/
