We often fight these questions when "various ligands" bind to our proteins. Generally, even if we know it's not water but an unidentified ligand which cannot be properly modeled or we are not brave enough to place it in the density we leave majority of the density uninterpreted but DO model a few waters in the closest H-bonding positions to protein. If the ligand was not there water would probably occupy that space anyway and who knows - may be our "ligand" is present only 50% and the other 50% is water ...
Modeling more UNKNOWN atoms might be the future for these cases? Jan D. On Wed, Jun 15, 2011 at 7:01 PM, wtempel <wtem...@gmail.com> wrote: > Thank you everyone for your replies. The Nayal & Di Cera (1996) > paper may be what I had in mind. I was looking for some estimate of > how often water atoms are placed in protein models where they do not > belong, and I expected a relatively high percentage. Simply > extrapolating from the 0.01% water <-> sodium misassignments in that > paper, the problem does not appear as significant as my intuition told > me. > Here is what started our lab's discussion: > 1. crystal structure of 1000 aa residues with approx. 60% solvent > content, a little better than 3A resolution, mean B factor approx 75 > A**2. > 2. approx. 50 Fo-Fc peaks > 4*sigma in very reasonable polar > environments, BUT many of them with coinciding with 2Fo-Fc density > ONLY when contoured at <1*sigma > 3. an anomalous difference Fourier map (calculated with a high > resolution limit of 3.5A) shows >3*sigma peaks only for some metal > ions that I know are present in the structure. > My initial argument, outlined below, rests on these assumptions: > A1. a conservative 10% of "waters" in a typical crystal structure are > really something else. I have no evidence for this, just my own > experience of the rigor I apply when modelling waters. > A2. 0.5-2 waters per aa residue. Levitt&Park 1993. Structure 1: 223-6 > How should we treat/model the Fo-Fc peaks for this specific example? I > argue to either ignore them or model them as unknown atoms. They could > be noise. But if they are not, they are among the strongest > diffracting 10% of the expected number of solvent atoms. I have > reasonable doubt that they are all waters. Heck, based on my > assumptions, many of them probably ARE NOT water. > I welcome your opinions. > Wolfram Tempel > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
