While the B value in the starting model was fine. I did drop it to a reasonable value and it now seems to be behaving, was thinking about trying that before I posted. Since this was an MR determination I did check and the starting model B value was actually smaller then the surrounding residues. I guess some thing went odd with the first round of refinement.
Thank you for the suggestions. Len > On Aug 10, 2022, at 10:25 AM, Dale Tronrud <[email protected]> wrote: > > > A large B value with positive difference density sure implies a convergence > problem with the refinement. Was the B value extreme in your starting model? > (A starting B that is wildly too large or too small at the start may cause > it to become trapped in the refinement.) Maybe if you rerun your refinement > with a moderate starting value for the B you will end up a more sensible > result. > > The only other way to end up with a parameter that directly conflicts with > the difference density is a bad restraint, but that doesn't sound likely > based on your description. > > Dale Tronrud > > On 8/10/2022 7:59 AM, Thomas, Leonard M. wrote: >> Hello All, >> I have run into something odd. In working on a structure for one of the >> groups I work with regularly, on one of the cystine residues I have a very >> large positive density peak at the sulfur position. The B value is >> approximately 4 times the other values in the residue and on other cystine >> residues. The overall structure has 2 molecules in the asymmetric unit and >> the corresponding cystine on the other monomer is behaving as I would >> expect. There are no disulfides in the structure. >> The data were collected on 9-2 at SSRL and all three of the data sets we >> collected show the same thing, all data go to about 2.2 angstroms. We are >> trying to determine the ligand binding in the molecule but this cystine is >> not involved in ligand binding. In house and other synchrotron data from >> previous protein preps and data collection runs of the same molecule grown >> in very similar condition and crystallized in the same space group have the >> residue behaving normally. >> I am open to any ideas as to what may be going on as I am rather puzzled by >> this. >> Thanks for any input, >> 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 >> [email protected] <mailto:[email protected]> >> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl >> <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://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/
