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

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+fro... 2008 Jan;64(Pt 1):99-107. Epub 2007 Dec 5. Surprises and pitfalls arising from (pseudo)symmetry. Zwart PHhttps://www.ncbi.nlm.nih.gov/pubmed/?term=Zwart%20PH%5BAuthor%5D&cauthor=true&cauthor_uid=180944731, Grosse-Kunstleve RWhttps://www.ncbi.nlm.nih.gov/pubmed/?term=Grosse-Kunstleve%20RW%5BAuthor%5D&cauthor=true&cauthor_uid=18094473, Lebedev AAhttps://www.ncbi.nlm.nih.gov/pubmed/?term=Lebedev%20AA%5BAuthor%5D&cauthor=true&cauthor_uid=18094473, Murshudov GNhttps://www.ncbi.nlm.nih.gov/pubmed/?term=Murshudov%20GN%5BAuthor%5D&cauthor=true&cauthor_uid=18094473, Adams PDhttps://www.ncbi.nlm.nih.gov/pubmed/?term=Adams%20PD%5BAuthor%5D&cauthor=true&cauthor_uid=18094473. DOI: 10.1107/S090744490705531Xhttps://doi.org/10.1107/S090744490705531X Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 [email protected]mailto:[email protected] (214) 645-6383 (phone) (214) 645-6353 (fax) On Apr 12, 2018, at 8:38 PM, Tanner, John J. mailto:[email protected]> 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]mailto:[email protected] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] ________________________________ UT Southwestern Medical Center The future of medicine, today.