[ccp4bb] Refinement of low resolution structures

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

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Subject: Reseach Associate position
From: dirk {- dot -} kessler {- at -} VIE {- dot -} BOEHRINGER-INGELHEIM {- dot -} COM dirk {- dot -} kessler {- at -} VIE {- dot -} BOEHRINGER-INGELHEIM {- dot -} COM
Date: 2007-04-03

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Subject: Re: Refinement of low resolution structures
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-04-03

Subject: Refinement of low resolution structures
From: Paul Paukstelis paul {- at -} ICMB {- dot -} UTEXAS {- dot -} EDU
Date: 2007-04-03

Hi all,

I'm refining the structure of a complex at low resolution (4.5).
Certainly refinement at low resolution will become more common, but
there isn't a whole lot out there now to use as a guide. I've
incorporated most of the suggestions from DeLaBarre and Brunger, but I'm
looking for any other suggestions and I have a couple of specific questions.

I have independent, high resolution structures for both molecules of the
complex, and I got a nice solution from Phaser. There is 4-fold NCS
(45,000 atoms in the ASU). Because of the low resolution I have also
added manual restraints based on secondary structure of the individual
structures to help the observation/parameter ratio. So far, I have been
using tight NCS restraints in Refmac along with Babinet scaling for bulk
solvent, fixed B for the solvent, and isotropic refinement for B
factors. Currently, R=25.7 Rfree=30.0 and the difference between R and
Rfree has stayed pretty constant from starting values in the 40's. I
just loosened up the NCS and got a fairly significant drop in R
(21.3)but a less significant drop in Rfree (28.8). The maps seem
somewhat better with some possible ion sites getting stronger in the
difference map. Should I worry about the large R change relative to Rfree?

I also have some very strong density for a portion of a molecule
(missing in the original structure) that I can't model unambiguously at
this resolution. It is very likely in multiple conformations. I'm
guessing this is going to cause the R factors to bottom out and I'm
worried trying to push the R factors down without building this will
lead to a some distortion around this area. Any suggestions on how to
handle this?

Finally, what would you like to see in a paper as validation for the
correctness of a model at this resolution and phased by MR? Omit maps of
key features?

Yes, I am trying to get higher resolution data.
Thanks in advance.

--paul

--
Paul Paukstelis, Ph.D.
Research Associate
Institute for Cellular and Molecular Biology
The University of Texas at Austin
P: 512-471-4778, F: 512-232-3420
paul@icmb.utexas.edu

CCP4bb navigation

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

Next message:
Subject: Re: Refinement of low resolution structures
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-04-03