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[ccp4bb] Has anyone seen such density?
 

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CCP4bb <-- 2007 <-- September 2007 <-- 19 September 2007
Previous message:
Subject: Torsion restraints in refmac
From: Eckhard Hofmann eckhard {- dot -} hofmann {- at -} BPH {- dot -} RUHR-UNI-BOCHUM {- dot -} DE
Date: 2007-09-19 		Next message:
Subject: Re: arp/warp in p22121
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-09-19


Subject: Has anyone seen such density?
From: Miriam-Rose Ash ash {- at -} FMP-BERLIN {- dot -} DE
Date: 2007-09-19
Hi all,

I have a 1.8A structure for which I am in the final stages of refinement. In a critical hinge region there are two unknown molecules bound to my protein, which appear to induce the formation of a domain swap. I am totally out of ideas as to what this molecule could be. I have attached a a jpg of the offending region. The total length of the unknown molecule is ~4.4A. The environment is polar and solvent exposed.

The crystallisation condition was: 0.1 M HEPES, 18% polacrylic acid, MgCl2, pH 7.0. Cryoprotectant was 20% glycerol. I wish it hadn't been, but triton-X was used during cell lysis as were Roche Complete Mini Protease Inhibitor Cocktail Tablets.

Glycerol is of the correct length but after one round of refinement a strong negative difference density appears over the middle -OH group and R factors increase. In addition, any molecule which is alkane-based has serious clashes with the protein backbone (eg. glycerol or ethylene glycol, C2H6O2).

Has anyone seen similarly shaped density, or have any ideas what it could be?

Thanks a lot for your help guys, I'm very grateful for any suggestions.
All the best,
Miriam

PS. Also thanks to everyone who writes in publicly to the bb - it has been a great learning resource!


CCP4bb navigation

CCP4bb <-- 2007 <-- September 2007 <-- 19 September 2007
Previous message:
Subject: Torsion restraints in refmac
From: Eckhard Hofmann eckhard {- dot -} hofmann {- at -} BPH {- dot -} RUHR-UNI-BOCHUM {- dot -} DE
Date: 2007-09-19 		Next message:
Subject: Re: arp/warp in p22121
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-09-19


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