Hi Filip,
Would it be a worth-while exercise to make a histogram of the absolute
values of atomic displacements ? If the distribution is bimodal (as you
indicated that it may), then indicating statistical significance should be
much easier (and convincing ?).
My twocents,
Nicholas
On Mon, 21 Nov 2011, Filip Van Petegem wrote:
> Dear crystallographers,
>
> I have a general question concerning the comparison of different
> structures. Suppose you have a crystal structure containing a few
> domains. You also have another structure of the same, but in a different
> condition (with a bound ligand, a mutation, or simply a different
> crystallization condition,...). After careful superpositions, you notice
> that one of the domains has shifted over a particular distance compared to
> the other domains, say 1-1.5 Angstrom. This is a shift of the entire
> domain. Now how can you know that this is a 'significant' change? Say the
> overall resolution of the structures is lower than the observed distance
> (2.5A for example).
>
> Now saying that a 1.5 Angstrom movement of an entire domain is not relevant
> at this resolution would seem wrong: we're not talking about some electron
> density protruding a bit more in one structure versus another, but all of
> the density has moved in a concerted fashion. So this would seem 'real',
> and not due to noise. I'm not talking about the fact that this movement
> was artificially caused by crystal packing or something similar. Just for
> whatever the reason (whether packing, pH, ligand binding, ...), you simply
> observe the movement.
>
> So the question is: how you can state that a particular movement was
> 'significantly large' compared to the resolution limit? In particular,
> what is the theoretical framework that allows you to state that some
> movement is signifcant? This type of question of course also applies to
> other methods such as cryo-EM. Is a 7A movement of an entire domain
> 'significant' in a 10A map? If it is, how do we quantify the significance?
>
> If anybody has a great reference or just an individual opinion, I'd like to
> hear about it.
>
> Regards,
>
> Filip Van Petegem
>
>
--
Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
