[ccp4bb] how to model this density?

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CCP4bb <-- 2008 <-- January 2008 <-- 07 January 2008

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Subject: Re: How to refine large moleculars?
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-01-07

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Subject: Re: how to model this density?
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-01-07

Subject: how to model this density?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-07

Dear All:
I am refining a structure at 2.6 A reslution. The protein is expressed in
CHO cell, so it might be glycosylated.
While refining an Asn residue as shown in the figure of the attachment, I
found some strange density extended beyond the side chain of Asn. The sigma
level for the fofc map of the figure in the attachment is as high as 3.0. My
protein buffer is Tris and NaCl, and the reservior is PEG and NH4Cl. I
believe this is not water mlecules. Considering the residue is Asn, I guess
it might be carbohydrate.
Is this density like a carbohydrate molecule? How to model this density?
Thanks and Happy New Year.

--
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 <-- January 2008 <-- 07 January 2008

Previous message:
Subject: Re: How to refine large moleculars?
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-01-07

Next message:
Subject: Re: how to model this density?
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-01-07