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>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]. | ||
==Good Values for Free R== | |||
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. | 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" />: | Free R is positively correlated with [[resolution]]<ref name="validation4pdb" />: | ||
{| class="wikitable" | |||
|- | |||
! Resolution, Å | |||
! Median Free R<ref name="validation4pdb" /> | |||
! Free R - (Resolution/10) | |||
! Free R Best 25% | |||
! Free R Worst 25% | |||
|- | |||
| 1.0 | |||
| 0.15 | |||
| 0.05 | |||
| <0.14 | |||
| >0.17 | |||
|} | |||
* At resolution 1.0 Å, the median free R is about 0.15 ((R/10) + 0.05). | * At resolution 1.0 Å, the median free R is about 0.15 ((R/10) + 0.05). | ||
Revision as of 19:07, 18 October 2011
Free R (also called Rfree) "is generally considered the most useful global measure of model-to-data agreement"[1]. It is a statistical quantity introduced in 1992 by Axel T. Brünger[2] 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 cross validation.
Good Values for Free RGood Values for Free R
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[1]:
| Resolution, Å | Median Free R[1] | Free R - (Resolution/10) | Free R Best 25% | Free R Worst 25% |
|---|---|---|---|---|
| 1.0 | 0.15 | 0.05 | <0.14 | >0.17 |
- 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 AlsoSee Also
Content DonorsContent Donors
The initial contents of this page were adapted from the Glossary of ProteinExplorer.Org, with the permission of the principal author, Eric Martz. The Free R entry there was written primarily by Diana Ditmore.
Literature CitedLiterature Cited
- ↑ 1.0 1.1 1.2 Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lutteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. A new generation of crystallographic validation tools for the protein data bank. Structure. 2011 Oct 12;19(10):1395-412. PMID:22000512 doi:10.1016/j.str.2011.08.006
- ↑ Brunger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 1992 Jan 30;355(6359):472-5. PMID:18481394