R value: Difference between revisions
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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 | 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. 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. | 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<ref>Kleywegt, GJ, AT Brünger. 1996. Checking your imagination: applications of the free R value. Structure 4:897-904. [http://www.ncbi.nlm.nih.gov/pubmed/8805582 PubMed]</ref>. | 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<ref>Kleywegt, GJ, AT Brünger. 1996. Checking your imagination: applications of the free R value. Structure 4:897-904. [http://www.ncbi.nlm.nih.gov/pubmed/8805582 PubMed].</ref>. | ||
One famous pitfall that can result in a misleading R value is the addition of substantially more than one water molecule per amino acid. | 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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==Content Donors== | ==Content Donors== | ||
Portions of this page were adapted from the [http://proteinexplorer.org/igloss.htm Glossary of ProteinExplorer.Org], with the permission of the principal author, [[User:Eric Martz|Eric Martz]]. | |||
==Literature== | ==Literature== | ||
<references /> | <references /> | ||
Revision as of 02:39, 27 June 2008
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. 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[1].
One famous pitfall that can result in a misleading R value is the addition of substantially more than one water molecule per amino acid.
Content DonorsContent Donors
Portions of this page were adapted from the Glossary of ProteinExplorer.Org, with the permission of the principal author, Eric Martz.