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

[Diana Tomchick]

Hi,

“How high is too high?” depends upon a lot of factors in your data that are related to the pseudo symmetry but also to the potential presence of other problems (e.g., anisotropy).

Look at this very useful Acta Cryst D paper from Paul Adam’s group and read the section about translational pseudo symmetry (Section 3.2).

Acta Crystallogr D Biol Crystallogr.<https://www.ncbi.nlm.nih.gov/pubmed/?term=Surprises+and+pitfalls+arising+from+(pseudo)symmetry#> 2008 Jan;64(Pt 1):99-107. Epub 2007 Dec 5.
Surprises and pitfalls arising from (pseudo)symmetry.
Zwart PH<https://www.ncbi.nlm.nih.gov/pubmed/?term=Zwart%20PH%5BAuthor%5D&cauthor=true&cauthor_uid=18094473>1, Grosse-Kunstleve RW<https://www.ncbi.nlm.nih.gov/pubmed/?term=Grosse-Kunstleve%20RW%5BAuthor%5D&cauthor=true&cauthor_uid=18094473>, Lebedev AA<https://www.ncbi.nlm.nih.gov/pubmed/?term=Lebedev%20AA%5BAuthor%5D&cauthor=true&cauthor_uid=18094473>, Murshudov GN<https://www.ncbi.nlm.nih.gov/pubmed/?term=Murshudov%20GN%5BAuthor%5D&cauthor=true&cauthor_uid=18094473>, Adams PD<https://www.ncbi.nlm.nih.gov/pubmed/?term=Adams%20PD%5BAuthor%5D&cauthor=true&cauthor_uid=18094473>.
DOI:
10.1107/S090744490705531X<https://doi.org/10.1107/S090744490705531X>

Diana

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Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
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Diana.Tomchick at UTSouthwestern.edu<mailto:Diana.Tomchick at UTSouthwestern.edu>
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On Apr 12, 2018, at 8:38 PM, Tanner, John J. <TannerJJ at missouri.edu<mailto:TannerJJ at missouri.edu>> 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
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

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