Quick navigation: Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |    Advert   |   
 

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

Main steps:

   - Protein purification
   - Crystallisation

Special:

   - Programs for crystallography
   - X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

   - CCP4BB

CCP4bb navigation

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

PS you say the model is complete, but just as important how complete
is (are?) the data.

-- 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
>
ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd