Hello Jacob, that's correct, I'm only looking at the mathematical significance, not the biological one. I follow the same reasoning - it is highly improbably for all atoms to be skewed in the same direction.
In a case I'm currently looking at, I'm particularly dealing with cryo-EM data, not X-ray structures, but with the same underlying principles: what are the odds that all pixels of the map move together in the same direction? As mentioned for X-ray structures, a Luzzati analysis may give information about the positional errors, but there should be an increased resolution when comparing domain movements, because it's unlikely for all atoms to have an error in the same direction. Filip On Mon, Nov 21, 2011 at 2:16 PM, Jacob Keller < [email protected]> wrote: > 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] > ******************************************* > -- 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/
