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

Tue Apr 17 12:16:33 PDT 2018

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 <pafonine at lbl.gov>
To: Tanner, John J. <TannerJJ at missouri.edu>, phenixbb at phenix-online.org
<phenixbb at phenix-online.org>
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: tannerjj at missouri.edu
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fphenix-online.org%2Fmailman%2Flistinfo%2Fphenixbb&data=02%7C01%7Cmawhite%40utmb.edu%7C4389508070e8473b2ea708d5a16a2022%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C636592399538790326&sdata=H0D6e7muY9LVRReD7StNbDsbdnp4GzpQiXnA%2F1usn1A%3D&reserved=0
Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20180417/0aab731c/attachment-0001.htm>