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Sorry Bart, that was not clearly phrased from my side.
What I tried to say is during refinement I use as much data as possible,
then I cut back the resolution and rerefine, then table1 is generated
and the extra 0.2 A which were cut off are additionally deposited for
e.g. developers.
I hope that is clearer now ?
I just think that all recorded data should go to the PDB - I might be
alone with my opinion but I think it actually might be useful to others.
And yes all structures are deposited with structure factors & x
wavelength if it was a MAD or SAD data set.
Sorry for causing confusion.
Jürgen
Bart Hazes wrote:
Juergen Bosch wrote:
I agree with Bart in the "reviewing part" but during refinement I use
all available data, depending on NCS, completeness and redundancy it
might also be lower than 1 sigma but not lower than 0.5. I would
expect that XDS will have a better I/sigI versus e.g. HKL2000 - but
maybe somebody much wiser might comment on this.
Once the refinement is done Table 1 is adjusted to meet the
expectations of reviewers I/sigI and Rsym, but the stuff that goes to
the PDB will contain all data :-)
Maybe I don't understand you correctly but the role of Table 1 is to
describe the experimental data that was used to derive the model. You
can't use resolution X for refinement and then report statistics up to
resolution Y because it looks nicer. Reviewers should definately have
a problem with that procedure. If you think the model is better by
following your procedure, and I'm not saying it's not, then you should
be able to state it in the paper and refute any comments reviewers may
have.
Bart
Jürgen
Bart Hazes wrote:
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Taiana Oliveira wrote:
Hi everybody,
I would like for you to clarify me abou the I/sigma value. I found
articles saying that resolutions with value below 2.0 must be
discarded but that for maxium likelihood methods this rule may be
ignored. How to proceed? What values may be considered as limits in
this case?
In my experience a value of 2.0 is conservative and seems to be used
mostly to avoid arguments with reviewers. There is not a hard cutoff
value but I think you're likely ok to 1.5. As the I/SigI goes down
the information content gets lower but maximum likelihood shoult
account for that. Check Rfree in the highest resolution shell to
make sure there is at least some correlation between model and
observations.
Bart
==============================================================================
Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
==============================================================================
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-418
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4542
FAX: +1-206-685-7002
