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>
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