Hi Jack, Polygon tool is designed answer questions like "what Rwork, Rfree and Rfree-Rwork I expect at this resolution?". If focusing on R-factors only, then you can get a quick idea using a command line tool: phenix.r_factor_statistics 2.25 Histogram of Rwork for models in PDB at resolution 2.15-2.35 A: 0.123 - 0.144 : 36 0.144 - 0.165 : 442 0.165 - 0.187 : 1669 0.187 - 0.208 : 2782 *0.208 - 0.230 : 2023**<<< Your case ** 0.230 - 0.251 : 812* 0.251 - 0.273 : 165 0.273 - 0.294 : 19 0.294 - 0.316 : 5 0.316 - 0.337 : 3 Histogram of Rfree for models in PDB at resolution 2.15-2.35 A: 0.160 - 0.183 : 43 0.183 - 0.207 : 405 0.207 - 0.231 : 1485 0.231 - 0.255 : 2759 * 0.255 - 0.278 : 2216**<<< Your case* 0.278 - 0.302 : 861 0.302 - 0.326 : 142 0.326 - 0.350 : 36 0.350 - 0.373 : 7 0.373 - 0.397 : 2 Histogram of Rfree-Rwork for all model in PDB at resolution 2.15-2.35 A: 0.001 - 0.011 : 55 0.011 - 0.021 : 247 0.021 - 0.031 : 782 0.031 - 0.041 : 1597 * 0.041 - 0.050 : 2124**<<< Your case* 0.050 - 0.060 : 1716 0.060 - 0.070 : 912 0.070 - 0.080 : 316 0.080 - 0.090 : 131 0.090 - 0.100 : 76 Number of structures considered: 7956 So it looks like R-factors you have is what one would expect at this resolution. Pavel On 4/12/18 18:38, Tanner, John J. wrote:
Dear PhenixBB,
We have a crystal form that xtriage flags as having strong translational pseudo symmetry (Patterson peak 57% the height of the origin peak, p-value = 3E-5).
The space group is P21212. We can solve the structure with MR and refine to R=0.233 and R-free =0.276 at 2.25 Angstrom resolution. The maps look very good, but do not suggest major additional modeling that could be done to improve the structure and lower the R-factors. I know that one expects the R-factors from refinement to be higher when TPS is present, but my question is how high is too high? Has anyone done a study that shows the expectations for R-factors when TPS is present?
Thanks,
Jack
John J. Tanner Interim Chair, Department of Biochemistry Professor of Biochemistry and Chemistry Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: [email protected] mailto:[email protected] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A
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