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Re: [ccp4bb] negative difference density around sulphur and oxygen atoms
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: negative difference density around sulphur and oxygen atoms
From: Chris Meier crystallography {- at -} CHRISTOPHMEIER {- dot -} COM
Date: 2012-04-04		Next message:
Subject: Re: negative difference density around sulphur and oxygen atoms
From: Ian Tickle ianjt05 {- at -} GMAIL {- dot -} COM
Date: 2012-04-04


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

Hi Chris

I would say there's something very wrong if you're seeing -6 sigma
difference peaks at O atoms. I don't see how this can be explained by
radiation damage. I for one have never seen that before in a
structure where there weren't other obvious issues (or maybe I just
haven't looked hard enough).

I would try refining it with a different program, e.g. Buster, or even
a different version of Refmac (I use 5.6.x routinely, but I see
there's a 5.7.x now - Garib will no doubt have an opinion on which is
the best one to use). At least that will eliminate the software as
the origin of the problem: if it doesn't go away then we'll have to
think again.

Cheers

-- Ian

On 4 April 2012 16:16, 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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