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Re: [ccp4bb] How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?
 

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CCP4bb <-- 2008 <-- January 2008 <-- 18 January 2008
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Subject: Re: How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?
From: Andrew Gulick gulick {- at -} HWI {- dot -} BUFFALO {- dot -} EDU
Date: 2008-01-18 		Next message:
Subject: difference between I over sigma I and I over sd
From: Lu Yongzhi luyongzhi99 {- at -} 163 {- dot -} COM
Date: 2008-01-19


Subject: Re: How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?
From: Pietro Roversi pietro {- dot -} roversi {- at -} PATH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-01-18
Hello Sun,
Roman Hillig and I refined a mixture of ADP+PO4 and ATP in the active site of ARL2 - it is enough to exclude all contacts of the superposing ligands and let the occupancies refine. The protocol we followed is described in:

Hanzal-Bayer M, Renault L, Roversi P, Wittinghofer A, Hillig RC.
Free in PMC
The complex of Arl2-GTP and PDE delta: from structure to function.
EMBO J. 2002 May 1;21(9):2095-106.

Best of luck!

Pietro

writes:
> Hello everyone,
>
> I have a structure of intermediate state in which about half amount of ATP decomposed to AMP and pyrophosphate. The ATP and AMP + pyrophosphate have little difference in conformation, sharing the same electron density.
>
> I just gave them different residue ID and did the TLS and restrained refinement in CCP4i. It is hard to tell from the R-factor because they are only a very small part of the whole structure. Can anyone tell whether it is the correct way to do?
>
> Any suggestions are greatly appreciated.
>
> Thank you very much!
>
> Sincerely,
>
> Sun Tang
>
>
> ---------------------------------
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