Yes, well, actually i'm only a middle author on that paper for a good
reason, but I did encourage Rebecca and Stephan to use all the data.
But on a later, much more modest submission, where the outer shell
was not only weak but very incomplete (edges of the detector),
the reviewers found it difficult to evaluate the quality
of the data (we had also excluded a zone with bad ice-ring
problems). So we provided a second table, cutting off above
the ice ring in the good strong data, which convinced them
that at least it is a decent 2A structure. In the PDB it is
a 1.6A structure. but there was a lot of good data between
the ice ring and 1.6 A.
Bart Hazes (I think) suggested a statistic called "effective
resolution" which is the resolution to which a complete dataset
would have the number of reflectionin your dataset, and we
reported this, which came out to something like 1.75.
I do like the idea of reporting in multiple shells, not just overall
and highest shell, and the PDB accomodatesthis, even has a GUI
to enter it in the ADIT 2.0 software. It could also be used to
report two different overall ranges, such as completeness, 25 to 1.6 A,
which would be shocking in my case, and 25 to 2.0 which would
be more reassuring.
eab
Douglas Theobald wrote:
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/
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