Re: [ccp4bb] negative difference density around sulphur and oxygen atoms

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: negative difference density around sulphur and oxygen atoms
From: Ian Tickle ianjt05 {- at -} GMAIL {- dot -} COM
Date: 2012-04-04

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Subject: Re: negative difference density around sulphur and oxygen atoms
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2012-04-04

Radiation damage induced loss of definition of disulfide bridges, side
chain carboxylates, and certain histidine residues has been observed in
synchrotron-irradiated protein crystals. For example, see Weik et al.,
PNAS 2000, 97, 623. I have also seen a recent paper where radiation
damage of a bound protein ligand was apparently observed in a
synchrotron beam.

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: rrowlett@colgate.edu

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
>
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: negative difference density around sulphur and oxygen atoms
From: Ian Tickle ianjt05 {- at -} GMAIL {- dot -} COM
Date: 2012-04-04

Next message:
Subject: Re: very uninformative
From: Kevin Jin kevinjin {- at -} GMAIL {- dot -} COM
Date: 2012-04-04