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R-factors: Difference between revisions
→Relation between R and Rfree as a function of resolution
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==== Relation between R and R<sub>free</sub> as a function of resolution ==== | ==== Relation between R and R<sub>free</sub> as a function of resolution ==== | ||
* The PDBe provide a service to plot many different statistical properties in the PDB against other properties. The link is http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp . You can see that there is an option of RDiff which is the difference between R and R-Free for all structures that contain both data. Take a look at this first. There is a second parameter which you can set to resolution and this will allow you to draw a plot that you want. This will draw a 3D isometric plot which you can scale, and pick data points to view particular entries. | |||
* formula from Kleywegt and Jones (2002): R<sub>free</sub> = 1.065*R + 0.036 | |||
* plot with empirical data: http://xray.bmc.uu.se/gerard/supmat/rfree2000/rfminusr_vs_resolution.gif | |||
* many more plots: http://xray.bmc.uu.se/gerard/supmat/rfree2000 | |||
* harry plotter (java): http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html | |||
References: | References: | ||
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* GJ Kleywegt and TA Jones (2002). Homo Crystallographicus - Quo vadis? Structure 10, 465-472. (reprint from http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=65) | * GJ Kleywegt and TA Jones (2002). Homo Crystallographicus - Quo vadis? Structure 10, 465-472. (reprint from http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=65) | ||
== what kinds of problems exist with these indicators? == | == what kinds of problems exist with these indicators? == | ||