Just to clarify: I think the question is about the mathematical sense
of "significance," and not the functional or physiological
significance, right? If I understand the question correctly, wouldn't
the reasoning be that admittedly each atom in the model has a certain
positional error, but all together, it would be very unlikely for all
atoms to be skewed in the same direction?

Jacob

On Mon, Nov 21, 2011 at 4:04 PM, Filip Van Petegem
<[log in to unmask]> 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
>
> --
> Filip Van Petegem, PhD
> Assistant Professor
> The University of British Columbia
> Dept. of Biochemistry and Molecular Biology
> 2350 Health Sciences Mall - Rm 2.356
> Vancouver, V6T 1Z3
>
> phone: +1 604 827 4267
> email: [log in to unmask]
> http://crg.ubc.ca/VanPetegem/
>

--
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
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