[ccp4bb] elusive DNA density

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Dissolving s-adenosylhomocysteine
From: Ralf JAUCH jauchr {- at -} GIS {- dot -} A-STAR {- dot -} EDU {- dot -} SG
Date: 2007-11-06

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Subject: Re: elusive DNA density
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-11-07

Subject: elusive DNA density
From: Melody Lin xtalin2007 {- at -} GMAIL {- dot -} COM
Date: 2007-11-06

Dear all,

I've been working on a series of DNA-protein complex structures. In my
recently acquired data sets, I got almost no density for DNA if I do
molecular replacement or rigid body fitting with the protein structure,
although I am 100% sure I have DNA in the structure by indepenent means. If
I use models with DNA, I could find some DNA density with those data sets,
but as I refine the structure, the density became very poor. The resolutions
for those data sets are between 2.0-2.4 A. Also, if I use the scaled data
from synchrotron rather than the re-scaled data at home, I got better DNA
density, although for re-scaling, I used site parameters that I copied done
from synchrotron. The only differences between those two sets of scaled data
are: (1) the original scaled data take into account all reflections,
including high resolution data with low completeness/redundancy, which are
cut in the re-scaling; (2) error models were changed so chi squares for each
bin are 0.8-1.2 for re-scaling.

My (very naive) questions are: (1) Does the DNA density I saw in the cases
where I use models with DNA for MR/rigid body fitting only reflect model
bias? (2) are simulated annealing or cycles of coordinate/B factor
refinement enough to get rid of model bias? (3) Does weak DNA density have
to do with data processing?

Thanks very much for any suggestion,
Melody Lin

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Dissolving s-adenosylhomocysteine
From: Ralf JAUCH jauchr {- at -} GIS {- dot -} A-STAR {- dot -} EDU {- dot -} SG
Date: 2007-11-06

Next message:
Subject: Re: elusive DNA density
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-11-07