Although the effect should be quite small, is the wavelength in your reflection file consistent with the actual wavelength?
Another option is that specific filters on atom types were used in the TLS refinement. I would refine the models with another program (REFMAC/Buster/PDB-REDO) to see if the B-factor anomaly remains. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Daniel M. > Himmel, Ph. D. > Sent: Wednesday, August 2, 2023 17:06 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] High Temperature Factors with TLS > > 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 > <mailto:danielmhim...@gmail.com> > > URL : https://www.HimmelSciMedCom.com > > > > On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. <lmtho...@ou.edu > <mailto: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 <mailto: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 ######################################################################## 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/
