Re: [ccp4bb] Observation:parameter ratio

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

Previous message:
Subject: Re: Observation:parameter ratio
From: Dirk Kostrewa kostrewa {- at -} GENZENTRUM {- dot -} LMU {- dot -} DE
Date: 2009-09-23

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Subject: Re: Test of cryoconditions without X-rays or cryostream
From: Clemens Grimm Clemens {- dot -} Grimm {- at -} BIOZENTRUM {- dot -} UNI-WUERZBURG {- dot -} DE
Date: 2009-09-23

Subject: Re: Observation:parameter ratio
From: Pete Meyer pameyer {- at -} MCW {- dot -} EDU
Date: 2009-09-23

> Brunger, A., DeLaBarre, B., Davies, J. & Weis, W. X-ray structure
> determination at low resolution. ACTA CRYSTALLOGRAPHICA SECTION
> D-BIOLOGICAL CRYSTALLOGRAPHY 65, 128-133 (2009).
>
> The paper quotes Wayne Hendrickson (says "submitted") regarding
> "determinancy" point (i.e. where the number of observations becomes
> equal to the number of flexible torsions (of course, in this extreme
> case gemoetric restraints essentially become constraints and you don't
> refine B-factrors at all. With 50% solvent this is ~5.4A, and you are
> far from that limit.

From a quick glance at that paper (although not the "submitted" one),
it looks like this determinancy point may only apply to cases where
components from high resolution structures are being used at lower
resolution (independent components of a complex at high res vs the full
complex at low res). This may or may not apply to cases where an
initial model refined at higher resolution is not available, although
I'm leaning more towards the "not applicable" side at the moment (my
understanding was that some level of over-determination was required.
Exactly what minimum level of over-determination is required is
something I haven't been able to find out yet).

> It is rather surprising that any reviewer anywhere would have doubts
> about possibility to refine structural model at 3.4A. While I don't
> know what the referee said *exactly*, but he/she may be unaware of this
>
> http://www.rcsb.org/pdb/statistics/histogram.do?mdcat=refine&mditem=ls_d_res_high&minLabel=0&maxLabel=5&numOfbars=10&name=Resolution

At 3.4 Angstroms, refinement should definitely be possible. But I might
not point a reviewer at that histogram. Assuming "mdcat=refine" is
limiting results to entries that have been refined, that table has
entries in the 20 to 70 Angstrom range, where I'd have doubts about the
validity of any refinement done. So I'm not sure that the PDB is
filtering for cases of acceptable refinement vs any refinement at all
(I've seen REMARK lines in deposited entries where the authors reported
that the refinement statistics were not necessarily valid given the
resolution of the structure; it may be easier to do a few cycles of
refinement to satisfy deposition requirements than deposit an unrefined
structure at low resolution).

>
>
>
> On Wed, 2009-09-23 at 12:48 +0000, hugh morgan wrote:
>> Hi,
>> We are attempting to address a referees comment concerning our
>> data/parameter ratio for a 3.4 A structure. Although the ratio is only
>> 0.5, the R/Rfree is 25/29, which seems acceptable. Ideally I would
>> like to include a reference showing a graph or table of data:parameter
>> vs resolution but I have been unable to find such a paper. Please
>> could someone point me in the right direction.
>> Thanks in advance
>>
>> Hugh
>>
>> P.S. It would be nice to know if this table has been published
>> http://www-structmed.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html
>>
>> or something similar to this, which includes higher resolution
>> structures
>> http://dirac.cnrs-orleans.fr/plone/Members/hinsen/data-parameter-ratio-in-x-ray-structure-determination
>>
>>
>>

CCP4bb navigation

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

Previous message:
Subject: Re: Observation:parameter ratio
From: Dirk Kostrewa kostrewa {- at -} GENZENTRUM {- dot -} LMU {- dot -} DE
Date: 2009-09-23