Hello,
B-factors actually do have a physical meaning which is at least to some
extent reflected by the crystal structures as refined. This can be
demonstrated at higher resolution structures: when we created three
tiers of structures, better than 1.9 Å, 1.9-2.4 Å, and 2.4-3.0 Å,
structures in the first one showed distinct distributions of B factors
for the amino acid side chain/main chain atoms inside and outside the
protein, for DNA bases, and phosphates, and for water at the interface,
and on the biomolecule surface. The distinction is less clear for the
1.9-2.4 Å structures and is lost completely below that resolution limit.
We think that the distributions for the high resolution structures can
be developed into meaningful set of constraints and/or validation criteria.
If interested, you can read more in our open access paper Acta Cryst.
(2014). D70, 2413–2419 (doi:10.1107/S1399004714014631).
Best regards,
Bohdan, bs.structbio.org
On 2020-03-11 16:41, Gerard DVD Kleywegt wrote:
If this is the case, why can't we use model B factors to validate our
structure? I know some people are skeptical about this approach
because B factors are refinable parameters.
Rangana
It is not clear to me exactly what you are asking.
B factors _should_ be validated, precisely because they are refined
parameters
that are part of your model. Where have you seen skepticism?
Rangana said that B-values should not be used *to validate structures*,
NOT that B-values themselves shouldn't be validated themselves.
I suppose I am at least in part to blame for the former notion and the
reason for this (at least circa 1995 when the Angry Young Men from
Uppsala first starting harping on about this) was that B-values tend(ed)
to be error sinks which could "absorb" all sorts of errors and phenomena
in addition to modelling atomic displacement (e.g., unresolved disorder,
unresolved NCS differences, incorrect restraints, incorrect atom types
modelled, partial ocupancies, etc.).
--Gerard
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Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
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Little known gastromathematical curiosity: let "z" be the
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of that pizza is equal to pi*z*z*a !
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