Re: [ccp4bb] One little clash

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: One little clash
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2012-07-11

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Subject: Re: One little clash
From: Jens Kaiser kaiser {- at -} CALTECH {- dot -} EDU
Date: 2012-07-12

Subject: Re: One little clash
From: Herman {- dot -} Schreuder {- at -} SANOFI {- dot -} COM Herman {- dot -} Schreuder {- at -} SANOFI {- dot -} COM
Date: 2012-07-12

Hi Christine,

Although difficult to judge from a static picture, to me the density
looks like two superimposed tyrosines. The only way to find out is to
try to model and refine them. In Refmac, sterice clashes should (!) be
switched off by the program if the the combined occupancy of the
residues involved is less than or equal 1. You could set the occupancies
of the tyrosine side chains to say 0.5 (or 0.49 to be safe) by editing
the PDB file. If you use buster you can use the EXCLUDE keyword in the
gelly file to switch off steric repulsions.

Since the two side chains cannot be phyisically at the same time at the
same position in space, there must be alternative conformations.
However, if those alternative conformations are truely disordered, you
may see nothing in the electron density maps, especially if you have
high resolution data, when the refinement programs have no possibilities
to fudge fake density by introducing model bias.

my 2 cents,
Herman

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Lukacs, Christine
Sent: Wednesday, July 11, 2012 9:38 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] One little clash

Hi all-

I have a protein that crystallizes in I422, and diffracts well,
between 1.3-1.7A. Beautiful density, slightly higher final R-factors
than you might expect at this resolution (low to mid 20s). The density
is all beautiful, except that I have this one little clash, between a
few atoms from a tyrosine and its symmetry mate. In this picture I have
it modeled as an Alanine and you can see the two tyrosine rings
interlocking; and there is clearly no alternate conformation.

Since it is not near my site of interest, I have been pretty
much ignoring it, going through refinement with it as an alanine, then
changing it at the very end to a tyrosine and just minimizing B-s, no
positional. Now that I plan to publish a bunch of these, I should
probably figure out what is really going on. Any insights?

Thanks

Christine

Christine Lukacs
Roche

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: One little clash
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2012-07-11

Next message:
Subject: Re: One little clash
From: Jens Kaiser kaiser {- at -} CALTECH {- dot -} EDU
Date: 2012-07-12