Pavel,

I have an issue with the general use of these metrics as an "IQ score" for protein structures. They completely ignore the details of the experimental data and use one value, the maximum resolution, to set the Bar. There are at least two reasons that this can be a poor choice. (1) Highly Anisotropic data may go to 2.8A along one cell axis, but only to 3.4A for the other two. (2) The parameters used to cut the data. Previously and I/sigma~3 or an Rmerge~30% were considered the limits of usable data. Today many data sets use a CC1/2>=0.5 as a cutoff, with will include significantly more high resolution data and push the "Resolution" to a higher value. In both cases we are now comparing data sets with data to ~1 I/sigma to older data sets with an cutoff I/sigma of ~ 3 - 5. These are not meaningful comparisons. If the software were to define a comparative resolution based on I/sigma, completeness, then these comparisons would be more meaningful.

If you want to reexamine the use of a single 'factor' in evaluating anything I can highly recommend Stephen Jay Gould's the Mismeasure of Man. We need to examine the assumptions that are made in the creation of these metrics.

--
Yours sincerely,

Mark A. White, Ph.D.
Associate Professor of Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
Macromolecular X-ray Laboratory,
Basic Science Building, Room 6.658A
University of Texas Medical Branch
Galveston, TX 77555-0647
mailto://[email protected]
http://xray.utmb.edu

QQ: "I suppose it is tempting, if the only tool you have is a hammer, to treat everything as if it were a nail."
- Abraham Maslow (1966)

-----Original Message-----
From: Pavel Afonine <[email protected]>
To: Tanner, John J. <[email protected]>, [email protected] <[email protected]>
Subject: Re: [phenixbb] R-factor expectations when translational pseudo symmetry is present
Date: Fri, 13 Apr 2018 11:11:59 -0700

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]
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

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

Office: Schlundt Annex 203A

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