[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 Elegheert
Ph.D. Student

Unit for Structural Biology&  Biophysics

Lab for Protein Biochemistry and Biomolecular Engineering
Department of Biochemistry&  Microbiology
Ghent University, Belgium

e-mail: jonathan.elegheert at ugent.be

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