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Re: [ccp4bb] unknown symmetric density
 

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CCP4bb <-- 2008 <-- February 2008 <-- 26 February 2008
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Subject: Facility Manager Opening, University of North Carolina
From: "Edward J {- dot -} Collins" collins1 {- at -} MED {- dot -} UNC {- dot -} EDU
Date: 2008-02-26 		Next message:
Subject: Re: unknown symmetric density
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2008-02-26


Subject: Re: unknown symmetric density
From: Mario Sanches msanches {- at -} LNLS {- dot -} BR
Date: 2008-02-26
Same thing to me. I was able to assign a PEG molecule to a similar density.

Mario Sanches

Jiamu Du wrote:

> Oh......
> Thank you. I will try to fit it with a piece of PEG.
> Best wishes.
>
> On Tue, Feb 26, 2008 at 10:38 PM,
> > wrote:
>
> Hi Jiamu,
>
> This is almost surely a nic piece you PEG3350.
>
> Regards,
>
> zsolt
>
>
> Dr. Zsolt Bocskei
> sanofi-aventis
> Chemical Sciences Department
> 16 rue d'Ankara
> 67000 Strasbourg
> France
>
>
> ------------------------------------------------------------------------
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *On Behalf Of *Jiamu Du
> *Sent:* Tuesday, February 26, 2008 3:33 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] unknown symmetric density
>
> Dear All,
> Here I am refining a 2.0 angstrom resolution structure of a
> protein in complex with a 18mer peptide. Now the refined model has
> a R/Rfree value of 0.206/0.266. But there is no obvious density
> for the peptide. An interesting observation is that some strange
> density is located in the proposed protein-peptide interaction
> interface as shown in the attachment. The shown map is SACO map at
> 1.0 sigma level. The strange density is near the 2-fold axis of
> the crystal cell, so the density is also 2-fold symmetric.
> Although I traced it with solvent molecules, I believe it is not.
> It seems not the peptide, either. But I can not image what it is.
> What do you think?
> The crystal condition contains Tris, Hepes, NaCl, ZnAc, and PEG3350.
> Thanks.
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)
>
>
>
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)



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