R value
The R value is used to assess progress in the refinement of a model from X-ray crystallographic data, and can be used as one factor in evaluating the quality of a model[1][2]. R is a measure of error between the observed intensities from the diffraction pattern and the predicted intensities that are calculated from the model. R values of 0.20 or less are taken as evidence that the model is reliable.
As a rule of thumb, models with R values substantially exceeding (resolution/10) should be treated with caution. Thus, if the resolution of a model is 2.5 Å, that model's R value should not exceed 0.25. Completely erroneous models (e.g. random models) give R values of 0.40 to 0.60.
However, R values themselves must be treated with caution. Unlike the Free R, acceptable R values can be achieved despite serious errors in the model, as demonstrated unequivocally by Kleywegt & Brünger[3].
One famous pitfall that can result in a misleading R value is the addition of substantially more than one water molecule per amino acid.
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This page was adapted from the Glossary of ProteinExplorer.Org, with the permission of the principal author, Eric Martz.
LiteratureLiterature
- ↑ Laskowski, Roman A. 2003. Structural quality assurance. Chapter 14 in Structural Bioinformatics (2003) edited by Philip E. Bourne and Helge Weissig, Wiley-Liss, 649 pages. Complete contents at structuralbioinformaticsbook.com.
- ↑ Kleywegt, GJ. 2000. Validation of protein crystal structures. Acta. Crystallogr. D. Biol. Crystallogr. 56:249-265
- ↑ Kleywegt, GJ, AT Brünger. 1996. Checking your imagination: applications of the free R value. Structure 4:897-904. PubMed