I have also seen a recent paper where radiation damage of a bound protein ligand was apparently observed in a synchrotron beam.
That was a manuscript were I would have happily given the coordinates and structure factors to the reviewers with my blessing. Learned a valuable lesson about adopting orphaned data sets though.
Cheers,
Katherine
I look forward to hearing from others how best to handle this in refinement.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
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Hamilton, NY 13346
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On 4/4/2012 11:16 AM, Chris Meier wrote:
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
