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 <[email protected]> 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: [email protected] > http://crg.ubc.ca/VanPetegem/ > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
