All statistics aside, I never believe a molecular 
replacement solution until it produces an Fo-Fc 
map with peaks for something that should have 
been there but wasn't in the model.

If you know roughly where the DNA should bind, 
you could try making a solvent mask that includes 
that region (plus the protein of course), and 
then see if you can pull up some vaguely 
believable density by density modification.

Do the crystals pack reasonably without the DNA there?

If you think the DNA is poorly ordered or at low 
occupancy, the most definitive test would 
probably be to collect a new set with iodine on 
the DNA.  If that doesn't show up, you're sunk!

Good luck,
Phoebe

At 02:08 AM 11/7/2007, Serge Cohen wrote:
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>Hi;
>
>You might also consider if it is likely that you have statistical
>disorder, causing a blur in the DNA. This could be the case if your
>binding is not specific, in which case it is possible that DNA is
>shifted by a couple of bases (or if your DNA is "nearly palindromic"
>you might have some AsU containing the DNA in one direction and other
>in the reverse direction).
>
>Obviously, for this to be the reason of the weak density you observe,
>you should first rule out the model bias introduced by MR (as
>mentioned by Debanu), an dalso consider what is the sequence of your
>DNA, it's structure, and the likeliness that it is not bound to the
>same way to the protein in each copy.
>
>Serge.
>
>PS : If you expect the DNA to be making some fibbers in the crystal,
>you should definitely be able to see from the diffraction images that
>you DNA is present by a strong SF along the fibber axis around the
>base stacking distance. This would also be a good proof that you
>indeed have diffracting DNA.
>
>Le 7 nov. 07 à 04:36, Melody Lin a écrit :
>
>>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
>
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---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
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