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
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



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