The high peak is to be expected if the B factor is ludicrously too high. I think the problem is in the behavior of the B factor refinement. Try setting all B factors for the CYS to some sensible value (you can do that in COOT - ) then see what happens after more cycles of refinement..
Eleanor On Wed, 10 Aug 2022 at 17:09, Tristan Croll <ti...@cam.ac.uk> wrote: > I've seen this happen with B-factor refinement reasonably often. As I > understand it the basic problem is that for small B-factors the gradient > d(density)d(B) is large, but for large B-factors the gradient is small. So > if the starting B-factor on an atom is very low and substantially lower > than what the density supports, then the first refinement cycle can > overstep to the point where there's almost no gradient, so future > refinement steps don't pull it back down. Tightening the B-factor > similarity restraints to surrounding atoms can help. > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Thomas, > Leonard M. <lmtho...@ou.edu> > *Sent:* 10 August 2022 17:01 > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* Re: [ccp4bb] Odd Positive Density Around a Cystine > > 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 <de...@daletronrud.com> > 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 > >> lmtho...@ou.edu <mailto:lmtho...@ou.edu <lmtho...@ou.edu>> > >> > 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