This could well be due to radiation damage - S are often affected, also Glu
and Asp side chains. It is hard to know what to do since the effects are
time related. If you have high redundancy maybe you could not use he later
batches? Otherwise maybe just relax the B factor restraints and let them
show the loss of atoms.. The trouble with that is that you have to relax
all side-chain B restraints which may not be so appropriate for ILE say...
Eleanor
On Apr 4 2012, Chris Meier wrote:
MessageDear all, I am refining the X-ray structure of a protein:Data to
~2A were collected at a latest-generation synchrotron.The 2fo-Fc maps are
crisp, the model of the protein is complete and I am reasonably happy
with the stats (R below 20%, Rfree below 25% in Refmac 5.5). However, I
am seeing a lot of negative difference density, especially around sulphur
atoms (negative density around -9 sigma) and oxygen atoms (e.g.
side-chain oxygens of Glu, Asp, etc. residues with negative density
around -6 sigma). Has anyone observed this before? I have found CCP4bb
postings discussing radiation damange of suplphur atoms(e.g.
http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html
).Can this also happen with oxygen atoms? What would be an appropriate
way to deal with this issue during refinement? Suggestions greatly
appreciated. Thanks,Chris
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
