One possible explanation for high B-factors, assuming the coordinates are refined correctly, is partial occupancy and high mobility (dynamics) at those heavy atom sites.
Also, one should check Fo-Fc maps of those positions. Are other atom types substituting for some of those heavy atoms (such as sulfate instead of phosphate)? Daniel ___________ Daniel M. Himmel, Ph. D. Principal, Himmel Sci Med Com, LLC E-mail : danielmhim...@gmail.com URL : https://www.HimmelSciMedCom.com On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. <lmtho...@ou.edu> wrote: > Hello All, > > A general questions though phenix.refine is being used for refinement. A > student I am working with has a structure that was solved and initially > refined using TLS and NCS parameters. They were given the structure to > gain some experience in refinement and they have been asking me some > questions, I was not involved in the initial work. While everything seems > to be happy and the model is correct with good refinement statistics for > the most part one thing that I am unsure of is some of the heavier atoms > (Phosphate and Sulfer) have very high temperature factors when looking at > individual residues or ligands. The temperature factors are at least twice > as high as the lighter atoms they are associated with. > > I am at a loss to explain what is going on, I really have not used TLS > refinement a lot so there is that. Resolution is about 2.5 angstroms with > good completeness. > > Thoughts? > > Thank You in advance > Len Thomas > > Leonard Thomas, Ph.D. > Biomolecular Structure Core, Director > Oklahoma COBRE in Structural Biology > Price Family Foundation Institute of Structural Biology > University of Oklahoma > Department of Chemistry and Biochemistry > 101 Stephenson Parkway > Norman, OK 73019-5251 > Office: (405)325-1126 > lmtho...@ou.edu > http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
