Dear 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