Re: [ccp4bb] Normalization of B-factors
Just be careful when drawing conclusions from B-factors. If you look at the mathematical way that a B-factor modifies a structure factor, you can see that as a B-factor's numerical value increases, the corresponding structure factor's contribution to a calculated diffraction pattern is reduced. In other words, an error in the atomic model (such as in model bias errors) can be masked by B-factor refinement. Thus, if you want to draw conclusions from B-factors, one must assume that the all parts of a structure have been uniformly refined well (carefully and mostly correctly). Having at least several similar structures that were refined independently and give the same general result can add confidence to an observed trend in B-factors over different parts of a structure. Making a comparison between different structures refined independently is one reason for normalization of B-factors. TLS might indeed be a better way to go. In any case, if you are exploring the relative mobility or degree of disorder of different parts of a structure, it would be a good idea to use an independent measure of flexibility in addition to the crystallographic result, such as H-exchange. -Daniel On Fri, Aug 10, 2018 at 5:21 AM, Gert Vriend wrote: > TLS groups are a good way to reduce the R-factor without doing very stupid > things. They give a better fit of coordinates to the data, so, when done > well, you get a better description of reality without (hopefully) > over-fitting. Most times, I think, TLS groups are defined by the > experimentalist and it is rather easy to have some residues in a TLS group > that perhaps better should not have been in that group. In practice this > seems not to be a big problem, but when you are going to use TLS parameters > to compare mobility reduction it seems worth thinking about these problems. > > That's why we made the BDB (http://www.cmbi.umcn.nl/bdb/), a database in > which we (for about 80% of the whole PDB) calculated isotropic B-factors > for all atoms. Those isotropic B-factors might also not be the best thing, > but when studying mobility aspects of proteins they will work better than > either looking at TLS values or looking as residual B-factors. > > Obviously, the BDB holds data only for deposited PDB files, but if anybody > contacts me outside the list we might be able to help. > > Gert > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Normalization of B-factors
TLS groups are a good way to reduce the R-factor without doing very stupid things. They give a better fit of coordinates to the data, so, when done well, you get a better description of reality without (hopefully) over-fitting. Most times, I think, TLS groups are defined by the experimentalist and it is rather easy to have some residues in a TLS group that perhaps better should not have been in that group. In practice this seems not to be a big problem, but when you are going to use TLS parameters to compare mobility reduction it seems worth thinking about these problems. That's why we made the BDB (http://www.cmbi.umcn.nl/bdb/), a database in which we (for about 80% of the whole PDB) calculated isotropic B-factors for all atoms. Those isotropic B-factors might also not be the best thing, but when studying mobility aspects of proteins they will work better than either looking at TLS values or looking as residual B-factors. Obviously, the BDB holds data only for deposited PDB files, but if anybody contacts me outside the list we might be able to help. Gert To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Normalization of B-factors
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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Re: [ccp4bb] Normalization of B-factors
I wouldnt have thought so. There is a B factor plot as part of CCP4I2 - does that show any pattern of differences between ligand and environ,ment? Eleanor On 9 August 2018 at 10:54, Santhosh Gatreddy wrote: > Hi all, > > I have to compare the B-factors of three of my ligand bound structures of > the same protein which were diffracted to 1.85, 1.98 and 2.01 A resolution. > > Is it necessary to normalize the B-factors of these structures (dimer in > ASU) before comparing them to understand the ligand induced stability. > > > Thanks for Your suggestions, > > Santhosh > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Normalization of B-factors
Hi all, I have to compare the B-factors of three of my ligand bound structures of the same protein which were diffracted to 1.85, 1.98 and 2.01 A resolution. Is it necessary to normalize the B-factors of these structures (dimer in ASU) before comparing them to understand the ligand induced stability. Thanks for Your suggestions, Santhosh To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
