[phenixbb] refinement at 4.4 A => side chains or not

Kendall Nettles knettles at scripps.edu
Fri Feb 12 09:23:13 PST 2010

I just did something similar for a data set that is around 3.5angstroms, using two components for molecular replacement from 2angstrom structures. I left side chains for the molecular replacement and first round of refinement/model building. After that I decided to keep side chains if there was electron density covering at least the alpha-carbon.
Kendall Nettles

On 2/12/10 12:18 PM, "Randy Read" <rjr27 at cam.ac.uk> wrote:

On the question of whether or not to leave in the side chains, I would say that you're pretty certain they're in the right place if they're where the MR calculation put them, so you should be as justified in leaving the side chains in as the main chain!  Taking them out would degrade the quality of your model.  If something needs to move (as indicated by difference maps), then you will have to be extremely careful not to over-interpret things.

If you're thinking in terms of information content then, when you're doing molecular replacement, much of your information comes from prior knowledge.  That's even more true at low resolution than at high resolution.


Randy Read

On 12 Feb 2010, at 17:04, jonathan elegheert wrote:

> 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
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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