[phenixbb] R-factor expectations when translational pseudo symmetry is present

[Pavel Afonine]

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: tannerjj at missouri.edu <mailto:tannerjj at missouri.edu>
> 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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