Re: [ccp4bb] Density for pyrophosphate?

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

Previous message:
Subject: Re: Density for pyrophosphate?
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-07-19

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Subject: Re: Density for pyrophosphate?
From: Junyu Xiao junyu {- at -} UMICH {- dot -} EDU
Date: 2009-07-20

Subject: Re: Density for pyrophosphate?
From: Charlie Bond Charles {- dot -} Bond {- at -} UWA {- dot -} EDU {- dot -} AU
Date: 2009-07-20

Could it be MPD (2-methyl-2,4-pentanediol)?

Cheers,
Charlie

Junyu Xiao wrote:
> Dear all,
>
> I am at the late stage of refining a 1.97 A structure. There is something
> in the ligand binding pocket, and I am not sure what it is exactly. Since
> this protein can potentially generate pyrophosphate from ATP, and I have
> ATP in the protein solution, so I tried to fit in a pyrophosphate. The
> Rwork/Rfree after refinement are 0.198/0.243. Below is the refined map. The
> 2fofc map looks ok (contoured at 1 sigma), however, there is always some
> red density around the pyrophosphate in the fofc map (contoured at 3
> sigma). I have also tried to fit in the density as two free phosphates, and
> the results are worse. Can I get some advices on this? Any suggestion will
> be greatly appreciated.
>
> Best regards,
> Junyu

--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
Charles.Bond@uwa.edu.au
+61 8 6488 4406

CCP4bb navigation

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

Previous message:
Subject: Re: Density for pyrophosphate?
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-07-19

Next message:
Subject: Re: Density for pyrophosphate?
From: Junyu Xiao junyu {- at -} UMICH {- dot -} EDU
Date: 2009-07-20