Dear Kay. Arguably, the resolution of a structure is the most important number to look at; it is definitely the first to be examined, and often the only one examined by non-structural biologists.
Since this number conveys so much concerning the quality/reliability of the the structure, it is not surprising that we need to get this one parameter right. Let us examine a hypothetical situation, in which a data set at the 2.2-2.0 resolution shell has 20% completeness. Is this a 2.0 A resolution structure? While you make a sound argument that including that data may result in a better refined model (more observations, more restraints), I would not consider that model the same quality as one refined against a data set that has >90% completeness at that resolution shell. As I see it, there are two issues here: one, is whether to include such data in refinement? I am not sure if low completeness (especially if not random) can be detrimental to a correct model, but I will let other weigh in on that. The second question is where to declare the resolution limit of a particular data set? To my mind, here high completeness (the term "high" needs a precise definition) better describes the true resolution limit of the diffraction, and with this what I can conclude about the quality of the refined model. My two cents. Arnon Lavie On Fri, April 18, 2014 6:51 pm, Kay Diederichs wrote: > Hi everybody, > > since we seem to have a little Easter discussion about crystallographic > statistics anyway, I would like to bring up one more topic. > > A recent email sent to me said: "Another referee complained that the > completeness in that bin was too low at 85%" - my answer was that I > consider the referee's assertion as indicating a (unfortunately not > untypical case of) severe statistical confusion. Actually, there is no > reason at all to discard a resolution shell just because it is not > complete, and what would be a cutoff, if there were one? What > constitutes "too low"? > > The benefit of including also incomplete resolution shells is that every > reflection constitutes a restraint in refinement (and thus reduces > overfitting), and contributes its little bit of detail to the electron > density map. Some people may be mis-lead by a wrong understanding of the > "cats and ducks" examples by Kevin Cowtan: omitting further data from > maps makes Fourier ripples/artifacts worse, not better. > > The unfortunate consequence of the referee's opinion (and its > enforcement and implementation in papers) is that the structures that > result from the enforced re-refinement against truncated data are > _worse_ than the original data that included the "incomplete" resolution > shells. > > So could we as a community please abandon this inappropriate and > un-justified practice - of course after proper discussion here? > > Kay > >
