Hi Roger,
personally, I would take the four dimers from Phaser, strip off all
side chains (make a poly-ala/gly), do a ML refinement with tight NCS
restraints. The resulting map could then be on-the-fly
real-space-averaged with Coot. At your resolution, I would expect to
see the real register of at least some side chains either in the
2mfodfc-map or in one of the real-space-averaged 2mfodfc-maps.
Good luck,
Dirk.
Am 01.09.10 17:12, schrieb Roger Rowlett:
[log in to unmask]" type="cite">
I am trying to find a MR solution for a large unit
cell (R3:H, 158x158x196) with a relatively poor, but I think
workable
search model (30% identity, 50% similarity). The data set is
decent to
2.4 A. I might be able to get better if necessary. I submitted
the
sequence of the target to the Phyre server, and it returned a PDB
file
derived from what I had already identified as the most likely
successful search model. Phaser finds a reasonable solution with
four
dimers (Z=9-15 depending on the data set) for which the unit cell
packing looks good. Phaser even assembles what looks like
"correct"
biological tetramers in the ASU and across the symmetry
interfaces. The
main chain appears to be mostly traceable, but the side chains are
not
all well-resolved, and I suspect from the better-defined regions,
that
the chain is misregistered by a residue or two throughout most of
the
structure.
Assuming that an MR solution is possible, what is a good approach
from
here? FWIW, Phaser does not correctly place a poly-Ala/Gly model,
although it may place three chains similarly to the MR solution I
have
with the Phyre model. My first thought is to:
1. Chainsaw the currrent solution, and attempt to identify and
build in
the correct register of the side chains. after refinement.
2. Do a low resolution refinement of the poly-Ala/Gly model to
better
thread the main chain?
3. Try EPMR with the Phyre model or the poly-Ala/Gly model
4. Give up and get real phases (but I'm so close now!?)
Thanks in advance.
--
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email:
[log in to unmask]
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [log in to unmask]
WWW: www.genzentrum.lmu.de
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