Another consideration here is your PDB deposition. If the reason for using weak data is to get a better structure, presumably you are going to deposit the structure using all the data. Then the statistics in the PDB file must reflect the high resolution refinement.
There are I think three places in the PDB file where the resolution is stated, but i believe they are all required to be the same and to be equal to the highest resolution data used (even if there were only two reflections in that shell). Rmerge or Rsymm must be reported, and until recently I think they were not allowed to exceed 1.00 (100% error?). What are your reviewers going to think if the title of your paper is "structure of protein A at 2.1 A resolution" but they check the PDB file and the resolution was really 1.9 A? And Rsymm in the PDB is 0.99 but in your table 1* says 1.3? Douglas Theobald wrote:
Hello all, I've followed with interest the discussions here about how we should be refining against weak data, e.g. data with I/sigI<< 2 (perhaps using all bins that have a "significant" CC1/2 per Karplus and Diederichs 2012). This all makes statistical sense to me, but now I am wondering how I should report data and model stats in Table I. Here's what I've come up with: report two Table I's. For comparability to legacy structure stats, report a "classic" Table I, where I call the resolution whatever bin I/sigI=2. Use that as my "high res" bin, with high res bin stats reported in parentheses after global stats. Then have another Table (maybe Table I* in supplementary material?) where I report stats for the whole dataset, including the weak data I used in refinement. In both tables report CC1/2 and Rmeas. This way, I don't redefine the (mostly) conventional usage of "resolution", my Table I can be compared to precedent, I report stats for all the data and for the model against all data, and I take advantage of the information in the weak data during refinement. Thoughts? Douglas ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` Douglas L. Theobald Assistant Professor Department of Biochemistry Brandeis University Waltham, MA 02454-9110 dtheob...@brandeis.edu http://theobald.brandeis.edu/ ^\ /` /^. / /\ / / /`/ / . /` / / ' ' '
