On Thursday, 09 August 2018 10:45:07 Pavel Afonine wrote:
> > I (personally) think the best answer from these was to look at the
> > TLS-subtracted residuals (ie. total B-factor - TLS component) — can’t
> > remember who sent it, off the top of my head.
> >
>
> TLS is just an approximation, sometimes good and sometimes not. If TLS
> parameters are refined along with individual ADPs ("residual") the latter
> tend to compensate for eventual inadequacy of TLS model.
>
> Pavel
Depending on the quality and resolution of your data, a different summary
may apply
If individual ADPs are refined along with a TLS model they may add
noise that obscures the significance of bulk motion and may
artifactually reduce R-factors through over-fitting.
The best method of comparing structures ultimately depends on what
question you are trying to answer.
If you are trying to document a reduction in overall flexibility due to
ligand binding, the TLS descriptions (rather than individual B factors)
may be the most informative thing to compare. If you are looking
for specific residues that become "locked down" or "disengaged"
upon ligand binding, then the opposite is true: you would want to
compare the residual B-factors in those residues after subtracting
out the TLS contribution.
At sufficiently high resolution you should also look for evidence
that some residues may gain or lose alternate conformations upon
ligand binding. High B factors may indicate that an alternate
conformation has been missed, or its occupancy may have changed.
Ethan
--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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