Free R: Difference between revisions
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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>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]. | [[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== | ==Good Values for Free R== | ||
As a rule of thumb, for models with [[resolution]] of 2.0 Å or better, free R should not exceed (resolution/10) by more than 0.05; that is, if the resolution is 2.0 Å, free R should not significantly exceed 0.25. For resolutions around 3.0 Å, 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 Å or better (Å values <2.0), free R should not exceed (resolution/10) by more than 0.05; that is, if the resolution is 2.0 Å, free R should not significantly exceed 0.25. For resolutions around 3.0 Å, 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" />: | Free R is positively correlated with [[resolution]]<ref name="validation4pdb" />: | ||
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|- | |- | ||
| ~4.0 | | ~4.0 | ||
| 0. | | 0.31 | ||
| <font color="red">- 0. | | <font color="red">- 0.09</font> | ||
| <0. | | <0.28 | ||
| >0.37 | | >0.35 | ||
|} | |||
:*Data in the above table for resolutions <= 3.5 Å 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 Å are based on 199 X-ray entries, for which free R values are given, with resolutions of 3.9-4.1 Å (Feb 2013). | |||
:*The median resolution for X-ray entries in the [[PDB]] is 2.07 Å (Feb 2013). | |||
==Bad Values for Free R== | |||
<!--In October, 2011, there are 79 X-ray crystallographic entries in the [[PDB]] deposited 1990 or later, with free R values of >= 0.40. The median resolution of these 79 entries is 4.2 Å.--> | |||
In October, 2011, there are 182 X-ray crystallographic entries in the [[PDB]] with free R values of >= 0.37. 45 of these have a resolution <= 3.0 Å, and 5 have a resolution of <= 2.0 Å. It seems likely that there are serious errors in most of these 45 models. | |||
In one amazing case, [[1zff]], the resolution is given as 0.94 Å, the R value as 0.428, and the free R as 0.444. | |||
==No Value for Free R== | |||
In October, 2011, there are 5,908 X-ray crystallographic entries in the PDB for which no free R value is given. These represent 8.8% of all 66,847 X-ray entries. Most of these were deposited before the free R methodology was described by Brünger in 1992<ref name="bruenger" />. | |||
:{| cellpadding="4" style="text-align: center; border: 1px solid darkgray;" | |||
|- style="background: #e0e0e0;" | |||
! Deposition Date | |||
! X-ray entries | |||
! No Free R | |||
|- | |||
| Through 1990 | |||
| 666 | |||
| 666 (100%) | |||
|- | |||
| 1991-1995 | |||
| 3,209 | |||
| 2,852 (89%) | |||
|- | |||
| 1996-2000 | |||
| 8,832 | |||
| 1,858 (21%) | |||
|- | |||
| 2001-2005 | |||
| 18,522 | |||
| 342 (1.8%) | |||
|- | |||
| 2006-<br>Oct 2011 | |||
| 35,618 | |||
| 190 (0.5%) | |||
|} | |} | ||
==See Also== | ==See Also== | ||