Recently we (I mean WE - community) frequently refine structures around 1 Angstrom resolution. This is not what for the Rfree was invented. It was invented to go away with 3.0-2.8 Angstrom data in times when people did not possess facilities good enough to look on the electron density maps…. We finish (WE - I again mean - community) the refinement of our structures too early.
Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 14, 2011, at 22:35 , Nat Echols wrote: > On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang <qqho...@gmail.com> wrote: > Sorry, I don't quite understand your reasoning for how the structure is > rendered useless if one refined it with all data. > > "Useless" was too strong a word (it's Friday, sorry). I guess simulated > annealing can address the model-bias issue, but I'm not totally convinced > that this solves the problem. And not every crystallographer will run SA > every time he/she solves an isomorphous structure, so there's a real danger > of misleading future users of the PDB file. The reported R-free, of course, > is still meaningless in the context of the deposited model. > > Would your argument also apply to all the structures that were refined before > R-free existed? > > Technically, yes - but how many proteins are there whose only representatives > in the PDB were refined this way? I suspect very few; in most cases, a more > recent model should be available. > > -Nat
