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Re: [ccp4bb] overlapping DNA in prt-DNA complex structure
 

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CCP4bb <-- 2008 <-- March 2008 <-- 10 March 2008
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Subject: overlapping DNA in prt-DNA complex structure
From: Sabine Schneider sabine {- dot -} schneider {- at -} CUP {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-03-10 		Next message:
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From: Marius Schmidt marius {- dot -} schmidt {- at -} PH {- dot -} TUM {- dot -} DE
Date: 2008-03-10


Subject: Re: overlapping DNA in prt-DNA complex structure
From: James Stroud jstroud {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2008-03-10
Both molecules are bound to the same piece of DNA and the DNA is along
the b-axis. Just drop one of the DNA duplexes.

James

On Mar 10, 2008, at 12:54 AM, Sabine Schneider wrote:

> Hello everyone,
>
> I am working on the structure of a protein-DNA complex with 2 mol/
> ASU. Data are to 2.8A and the symmetry appears to be orthorhombic
> (P212121; a=42.280 b=113.340 c=134.670) I solved the structure by
> moleculare replacement using the coordinates of the protein in
> phaser. I got relative good density for the DNA and started building
> for the DNA for one protein molecule and gave the model back to
> phaser. The statistics for the solution are very good (RFZ=16.7
> TFZ=27.8 PAK=0 LLG=820 RFZ=14.9 TFZ=42.9 PAK=0 LLG=2215 LLG=2215).
> My problem is now that the ends of the DNA strands of the two
> complexes in the asu are crashing by overlapping almost perfectly as
> well as with the symmetry related molecules. So instead of beeing
> able to fit in a 15mer, which was used in the crystallisation, I
> only can fit in maybe an 8mer (which is also not making really sense
> DNA-sequence wise). I tried reindexing to klh and lhk but same
> problem.
>
> Has anyone an idea how to solve this?
>
> Thanks a lot for your help!
>
> Sabine

--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
Los Angeles, CA 90095

http://www.jamesstroud.com




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CCP4bb <-- 2008 <-- March 2008 <-- 10 March 2008
Previous message:
Subject: overlapping DNA in prt-DNA complex structure
From: Sabine Schneider sabine {- dot -} schneider {- at -} CUP {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-03-10 		Next message:
Subject:
From: Marius Schmidt marius {- dot -} schmidt {- at -} PH {- dot -} TUM {- dot -} DE
Date: 2008-03-10


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