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 <[log in to unmask]> 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
>>
>> [log in to unmask]
>> http://theobald.brandeis.edu/
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>
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