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Re: [ccp4bb] unknown symmetric density |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 26 February 2008Subject: Re: unknown symmetric density From: Partha Chakrabarti ppchak {- at -} GMAIL {- dot -} COM Date: 2008-02-26 I have seen similar density once. Did you by any chance have PEG 400 in the cryo? If you are using coot, would be interesting if you get two PEGs from monomer library and that sort of make up for the density.. (two carbons less). Regards, Partha On Tue, Feb 26, 2008 at 2:32 PM, Jiamu Du > 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) -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra@nimr.mrc.ac.uk Phone: + 44 208 816 2515 CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 26 February 2008 |
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