[phenixbb] refinement at 4.4 A => side chains or not
jonathan elegheert
jonathan.elegheert at ugent.be
Fri Feb 12 09:04:38 PST 2010
Dear bb,
could anyone please share his/her opinion on following matter;
I am refining a 4.4 A protein complex structure which I could solve
using MR with the high resolution models of the separate components. I
also have another 3.5 A crystal form of the complex. My question is
whether or not to rebuild/leave "positionally known" side chains in the
4.4 A structure, because of course 2/3 of the time there is of course no
density for it. However, a review of the PDB learnes that almost all
models deposited between 4 and 5 A contain full side chains! Personally
my opinion is not to include them because a model should be a
representation of the information content of the experiment and thus
density, but maybe that deviates from the consensus.
On a more technical note: until now the trimming procedure has only
sporadically led to Fo-Fc 'blobs' in the hydrophobic protein interior;
are there proven modifications one has to apply to the bulk solvent
model mask to avoid these even more?
Thanks a lot for your insights,
Jonathan
--
Jonathan Elegheert
Ph.D. Student
Unit for Structural Biology& Biophysics
http://www.lprobe.ugent.be/xray.html
Lab for Protein Biochemistry and Biomolecular Engineering
Department of Biochemistry& Microbiology
Ghent University, Belgium
e-mail: jonathan.elegheert at ugent.be
More information about the phenixbb
mailing list