[ccp4bb] unknown symmetric density

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CCP4bb <-- 2008 <-- February 2008 <-- 26 February 2008

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From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-26

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Subject: Re: unknown symmetric density
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
Date: 2008-02-26

Subject: unknown symmetric density
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-02-26

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)

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CCP4bb <-- 2008 <-- February 2008 <-- 26 February 2008

Previous message:
Subject: Re: ccp4 6.0.2 installation error in Red Hat Enterprises 5.1
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-26

Next message:
Subject: Re: unknown symmetric density
From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM
Date: 2008-02-26