Free R: Difference between revisions

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[[Free R]] "is generally considered the most useful global measure of model-to-data agreement"<ref>PMID: 22000512</ref>. It is a statistical quantity introduced in 1992 by Axel T. Brünger<ref>~~Brünger AT. Free R value~~: ~~a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:472-5. [http://www.ncbi.nlm.nih.gov/pubmed/~~18481394 ~~PubMed]~~</ref> to assess the quality of a model from X-ray crystallographic data. It is calculated in the same manner as the [[R value]], but from a subset of the data set aside for the calculation of free R, and not used in the refinement of the model. It is a more reliable tool for assessing the model than the R value because it is not self-referential -- that is, as an estimation of errors, free R is free of any bias that may have been introduced during refinement. Free R is an example of the application of the more general method of [http://en.wikipedia.org/wiki/Cross-validation_(statistics) cross validation].

[[Free R]] (also called Rfree) "is generally considered the most useful global measure of model-to-data agreement"<ref name="validation4pdb">PMID: 22000512</ref>. It is a statistical quantity introduced in 1992 by Axel T. Brünger<ref>PMID: 18481394</ref> to assess the quality of a model from X-ray crystallographic data. It is calculated in the same manner as the [[R value]], but from a subset of the data set aside for the calculation of free R, and not used in the refinement of the model. It is a more reliable tool for assessing the model than the R value because it is not self-referential -- that is, as an estimation of errors, free R is free of any bias that may have been introduced during refinement. Free R is an example of the application of the more general method of [http://en.wikipedia.org/wiki/Cross-validation_(statistics) cross validation].

As a rule of thumb, free R should not exceed the R value by more than 0.05; that is, if the R value is 0.20, free R should not significantly exceed 0.25. Free R values exceeding 0.40 raise serious doubts about the model.

Free R is positively correlated with [[resolution]]<ref name="validation4pdb" />:

* At resolution 1.0 Å, the median free R is about 0.15 ((R/10) + 0.05).

* At resolution 1.5 Å, the median free R is about 0.21 ((R/10) + 0.06).

* At resolution 2.0 Å, the median free R is about 0.24. ((R/10) + 0.04) (The median resolution in the [[PDB]] is 2.06 Å [Oct 2011])

* At resolution 2.5 Å, the median free R is about 0.26. ((R/10) + 0.01)

* At resolution 3.0 Å, the median free R is about 0.28. ((R/10) - 0.01)

* At resolution 3.5 Å, the median free R is about 0.30. ((R/10) - 0.05)

==See Also==

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-[[Free R]] "is generally considered the most useful global measure of model-to-data agreement"<ref>PMID: 22000512</ref>. It is a statistical quantity introduced in 1992 by Axel T. Brünger<ref>Brünger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:472-5. [http://www.ncbi.nlm.nih.gov/pubmed/18481394 PubMed]</ref> to assess the quality of a model from X-ray crystallographic data. It is calculated in the same manner as the [[R value]], but from a subset of the data set aside for the calculation of free R, and not used in the refinement of the model. It is a more reliable tool for assessing the model than the R value because it is not self-referential -- that is, as an estimation of errors, free R is free of any bias that may have been introduced during refinement. Free R is an example of the application of the more general method of [http://en.wikipedia.org/wiki/Cross-validation_(statistics) cross validation].
+[[Free R]] (also called R<sub>free</sub>) "is generally considered the most useful global measure of model-to-data agreement"<ref name="validation4pdb">PMID: 22000512</ref>. It is a statistical quantity introduced in 1992 by Axel T. Brünger<ref>PMID: 18481394</ref> to assess the quality of a model from X-ray crystallographic data. It is calculated in the same manner as the [[R value]], but from a subset of the data set aside for the calculation of free R, and not used in the refinement of the model. It is a more reliable tool for assessing the model than the R value because it is not self-referential -- that is, as an estimation of errors, free R is free of any bias that may have been introduced during refinement. Free R is an example of the application of the more general method of [http://en.wikipedia.org/wiki/Cross-validation_(statistics) cross validation].
 As a rule of thumb, free R should not exceed the R value by more than 0.05; that is, if the R value is 0.20, free R should not significantly exceed 0.25. Free R values exceeding 0.40 raise serious doubts about the model.
+Free R is positively correlated with [[resolution]]<ref name="validation4pdb" />:
+* At resolution 1.0 &Aring;, the median free R is about 0.15 ((R/10) + 0.05).
+* At resolution 1.5 &Aring;, the median free R is about 0.21 ((R/10) + 0.06).
+* At resolution 2.0 &Aring;, the median free R is about 0.24. ((R/10) + 0.04) (The median resolution in the [[PDB]] is 2.06 &Aring; [Oct 2011])
+* At resolution 2.5 &Aring;, the median free R is about 0.26. ((R/10) + 0.01)
+* At resolution 3.0 &Aring;, the median free R is about 0.28. ((R/10) <font color="red">- 0.01</font>)
+* At resolution 3.5 &Aring;, the median free R is about 0.30. ((R/10) <font color="red">- 0.05</font>)
 ==See Also==