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Dear Filip 'Annoying' MR problems for which the answer often lies in relatively small differences between the search model and 'RB-shifted' domains and/or subdomains in the actual structure, are I think a good experimental indication of the significance of such issues. To extrapolate from this, RB refinement of whole domains that are initially misplaced by 0.5-2 angstroms will show that X-ray data to 4-8 angstrom resolution are often sufficient to refine the model to a position that decisively agrees better with data as judged by crystallographic refinement R-factors and electron density. So, my reaction every time I see such behavior is that the observed domain shift must be significant and that I should do my crystallographic best to model and cross-validate it as well as the data quality and resolution will allow. However, the biological interpretation and impact of such significant displacements are of course quite specific to the system under study. Best regards, Savvas On 21 Nov 2011, at 23:04, 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 > > -- > 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/