Hi Ed, Thanks for the comments. So what do you recommend? Refine against weak data, and report all stats in a single Table I?
Looking at your latest V-ATPase structure paper, it appears you favor something like that, since you report a high res shell with I/sigI=1.34 and Rsym=1.65. On Dec 6, 2012, at 7:24 PM, Edward A. Berry <ber...@upstate.edu> wrote: > 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/ >> >> ^\ >> /` /^. / /\ >> / / /`/ / . /` >> / / ' ' >> ' >> >> >
