[phenixbb] R-factor expectations when translational pseudo symmetry is present
Pavel Afonine
pafonine at lbl.gov
Fri Apr 13 11:11:59 PDT 2018
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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