So the Phosphates are actually the end of the ADP which the Sulfer atoms are Cystiene suffers. The Fo-Fc maps show large positive peaks for each position also. The TLS groups is the whole protein chain, there are 4 in the asymmetric unit as the biological unit I think is a dimer of 2 different chains. ADP and FAD are bound and are separate from what I can tell.
Len On Aug 2, 2023, at 10:05 AM, Daniel M. Himmel, Ph. D. <danielmhim...@gmail.com<mailto:danielmhim...@gmail.com>> wrote: 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<https://urldefense.com/v3/__https://www.HimmelSciMedCom.com__;!!GNU8KkXDZlD12Q!4grvWZPnBfhiVYZr36zWIWck7uhrTJOJaSvLQUxBWpRcVnX24AW4bD-1IRN-kHqzGzaAbv_QJgdCVPi16i4PTw$> On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. <lmtho...@ou.edu<mailto:lmtho...@ou.edu>> wrote: Hello All, A general questions though phenix.refine is being used for refinement. A student I am working with has a structure that was solved and initially refined using TLS and NCS parameters. They were given the structure to gain some experience in refinement and they have been asking me some questions, I was not involved in the initial work. While everything seems to be happy and the model is correct with good refinement statistics for the most part one thing that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) have very high temperature factors when looking at individual residues or ligands. The temperature factors are at least twice as high as the lighter atoms they are associated with. I am at a loss to explain what is going on, I really have not used TLS refinement a lot so there is that. Resolution is about 2.5 angstroms with good completeness. Thoughts? Thank You in advance Len Thomas Leonard Thomas, Ph.D. Biomolecular Structure Core, Director Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmtho...@ou.edu<mailto:lmtho...@ou.edu> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!GNU8KkXDZlD12Q!4grvWZPnBfhiVYZr36zWIWck7uhrTJOJaSvLQUxBWpRcVnX24AW4bD-1IRN-kHqzGzaAbv_QJgdCVPjPd0u6Hg$> ######################################################################## 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/
