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On Wed, Apr 4, 2012 at 10:31 AM, Roger Rowlett <[log in to unmask]> wrote: > 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 > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: [log in to unmask] > > > 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<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 >> >> >>