Hi Nukri,
Note that in the ultra-high resolution structure of aldose reductase http://www.ncbi.nlm.nih.gov/pubmed/15146478 we didn't see all (or most) hydrogens. So, the converse question one could ask is why we didn't see all of them? Was it only because of higher B-factors or because some of them were stripped during data collection?
yes, we saw ~54% of them - I used to work on this at some point too ( Blakeley MP, Ruiz F, Cachau R, Hazemann I, Meilleur F, Mitschler A, Ginell S, Afonine P, Ventura ON, Cousido-Siah A, et al. Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase. Proc Natl Acad Sci U S A.2008;105(6):1844--1848.)
My impression at that point was that we did not see the rest partially because the model was not "good enough" (in terms of seeing fine details). What I mean is that improving model from R-factor~10 to R~9% resulted in adding ~10% more visible H atoms. When I then refined the model down to ~7% using Interatomic Scatterers model (to account for deformation density) the amount of observable H atoms increased from published 54% up to ~68% or so (writing from memory). So, hypothetically, I guess, if we could refine it down to some lower R-factor we then would see even more H atoms (and the rest, if we finally don't see them - would probably be those that gone). The resolution and B-factors are necessary but not enough to see H atoms - the overall noise level is a key too.
All the best! Pavel.
