I agree with Artem. I also don't think you have a register problem.
All of the residues show typical 2fofc density for their types,
especially considering the 3A data. The disappearing act of the asp
carboxyl is typical of solvent exposed aspartates. Assuming the
register is correct, you have a carbonyl flip somewhere throwing off
the whole segment. The phe is telltale. The 2 dimensionality and
limited region of the picture makes a full diagnosis difficult.
Also, the 2fofc is heavily biased. Don't trust it when it tells you
where things are. I find 2fofcs essentially useless. Your milage may
vary.
James
On Aug 20, 2009, at 5:24 PM, Mike England wrote:
Hi all,
I will appreciate the comments on the 2Fo-Fc (1.5 sigma) and Fo-Fc
(3.0 sigma) (at coot) maps as shown in attached picture .
I am working at 3.0 A resolution (MR phasing with more than 80%
homology) and current Rfree is 0.27 and FOM of 0.8.
How to interpret the positive density (green) in Fo-Fc map which
overlaps with the C-alpha tube? The side-chains of the polypeptide
around this regions seems to be properly fitting and registry of the
sequence seems to be OK.
Is this due to some kind of model bias?
Thanks in advance.
Mike
<Picture 1.png>
