Free R: Difference between revisions

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Eric Martz, Eran Hodis

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 [[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 name="bruenger">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].
+==Help Interpreting Free R==
+When a crystallographic protein structure is visualized in [[FirstGlance/Index|FirstGlance in Jmol]], its Free R will be automatically interpreted as ''Reliability'' with the following levels, each relative to its [[Resolution]]:
+*<span style="color:#00e000;font-weight:bold;">Much better than average</span>
+*<span style="color:green;font-weight:bold;">Better than average</span>
+*<span style="color:black;font-weight:bold;">Average</span>
+*<span style="color:#a0a000;font-weight:bold;">Worse than average</span>
+*<span style="color:red;font-weight:bold;">Unreliable</span>
 ==Good Values for Free R==
-As a rule of thumb, for models with [[resolution]] of 2.0 &Aring; or better, free R should not exceed (resolution/10) by more than 0.05; that is, if the resolution is 2.0 &Aring;, free R should not significantly exceed 0.25. For resolutions around 3.0 &Aring;, the free R should not exceed (resolution/10). Free R values exceeding the worst 25% for the resolution of the model (see table below) raise doubts about the quality of the model.
+As a rule of thumb, for models with [[resolution]] of 2.0 &Aring; or better (&Aring; values <2.0), free R should not exceed (resolution/10) by more than 0.05; that is, if the resolution is 2.0 &Aring;, free R should not significantly exceed 0.25. For resolutions around 3.0 &Aring;, the free R should not exceed (resolution/10). Free R values exceeding the worst 25% for the resolution of the model (see table below) raise doubts about the quality of the model.
 Free R is positively correlated with [[resolution]]<ref name="validation4pdb" />:
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 |-
 | ~4.0
-| 0.32
+| 0.31
-| <font color="red">- 0.08</font>
+| <font color="red">- 0.09</font>
-| <0.30
+| <0.28
-| >0.37
+| >0.35
 |}
-**Data in the above table for resolutions <= 3.5 &Aring; are approximated from Figure 3C in <ref name="validation4pdb" />, based on X-ray entries deposited in the [[PDB]] since 1990.
+:*Data in the above table for resolutions <= 3.5 &Aring; are approximated from Figure 3C in <ref name="validation4pdb" />, based on X-ray entries deposited in the [[PDB]] since 1990.
-**Data for resolution ~4.0 &Aring; are based on 168 X-ray entries deposited 1990 or later with resolutions of 3.9-4.1 &Aring; (Oct 2011). For comparison, there were 677 entries with resolutions 3.4-3.6 &Aring;.
+:*Data for resolution ~4.0 &Aring; are based on 199 X-ray entries, for which free R values are given, with resolutions of 3.9-4.1 &Aring; (Feb 2013).
-**The median resolution for X-ray entries in the [[PDB]] is 2.06 &Aring; (Oct 2011).
+:*The median resolution for X-ray entries in the [[PDB]] is 2.07 &Aring; (Feb 2013).
 ==Bad Values for Free R==