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 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]. | [[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== | ||
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| ~4.0 | | ~4.0 | ||
| 0.31 | | 0.31 | ||
| <font color="red">- 0. | | <font color="red">- 0.09</font> | ||
| <0.28 | | <0.28 | ||
| >0.35 | | >0.35 | ||
| Line 71: | Line 79: | ||
:*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 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). | :*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. | :*The median resolution for X-ray entries in the [[PDB]] is 2.07 Å (Feb 2013). | ||
==Bad Values for Free R== | ==Bad Values for Free R== | ||