Nat Echols wrote:
On Sat, Jan 19, 2013 at 4:14 AM, Qixu Cai<caiq...@gmail.com> wrote:
Could you please teach me any method to present the relationship between
resolution and B values of all the x-ray structures in Protein Data Bank.
Can the PDB statistics in RCSB do it?
Perhaps, and I'm pretty sure PDBe has a similar service, and there are
probably at least a half-dozen other ways to get this information, but
it's basically just going to look like the attached plot. (Although
I'm not sure I trust some of the very-low-B-factor structures at low
resolution.)
-Nat
It might be good to look as a function of year deposited, since this seems
to be changing. Perhaps some of the low B-factors at low resolution were
obtained with ancient programs, or B-factor was not refined at all?
Gerard "CD" Kleywegt wrote:
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well, i had a quick look at the data stored in QDB
(gjk, acta cryst d52, 842-857) which shows that
for 435 structures the corr coeff between resolution
and average b is only 0.06, i.e. insignificant
the only non-trivial correlate (using a 0.2 cut-off)
is the percentage of secondary structure (makes
sort of sense) with cc=0.20
in my other large-scale test, mentioned a couple
of weeks ago, i found that essentially all temp-
factor-related staistics are "incorrectly"
correlated with measures of model accuracy
(e.g., higher average b tends to be accompanied
by higher accuracy !). average b is very strongly
correlated with completeness on the other hand.
i suspect that problems with data and/or restraints
(rather than physics) are a major determinant
of the temp-factors we calculate for our models ...
--dvd
On Thu, 4 Jan 2001, Yu Wai Chen wrote:
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Dear all,
Does any one know if there is any correlation between the overall
B-factor of a structure in relation to its resolution? Are there any
publications on this topic?
Also is there any correlation between the extent of disorder in a
structure and the R-factor/Rfree?
Thanks.
Wai
--
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Yu Wai CHEN, Ph.D. .................. email:y...@mrc-lmb.cam.ac.uk
Centre for Protein Engineering, tel:+44-(0)1223-402148
MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140
WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc
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Gerard J. Kleywegt
Dept. of Cell& Molecular Biology Bolshevik University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se
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