Pavel,
I have an issue with the general use of these metrics as an "IQ score"
for protein structures. They completely ignore the details of the
experimental data and use one value, the maximum resolution, to set the
Bar. There are at least two reasons that this can be a poor choice.
(1) Highly Anisotropic data may go to 2.8A along one cell axis, but only
to 3.4A for the other two. (2) The parameters used to cut the data.
Previously and I/sigma~3 or an Rmerge~30% were considered the limits of
usable data. Today many data sets use a CC1/2>=0.5 as a cutoff, with
will include significantly more high resolution data and push the
"Resolution" to a higher value. In both cases we are now comparing data
sets with data to ~1 I/sigma to older data sets with an cutoff I/sigma
of ~ 3 - 5. These are not meaningful comparisons. If the software were
to define a comparative resolution based on I/sigma, completeness, then
these comparisons would be more meaningful.
If you want to reexamine the use of a single 'factor' in evaluating
anything I can highly recommend Stephen Jay Gould's the Mismeasure of
Man. We need to examine the assumptions that are made in the creation
of these metrics.
--
Yours sincerely,
Mark A. White, Ph.D.
Associate Professor of Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
Macromolecular X-ray Laboratory,
Basic Science Building, Room 6.658A
University of Texas Medical Branch
Galveston, TX 77555-0647
mailto://[email protected]
http://xray.utmb.edu
QQ: "I suppose it is tempting, if the only tool you have is a hammer, to
treat everything as if it were a nail."
- Abraham Maslow (1966)
-----Original Message-----
From: Pavel Afonine
Dear PhenixBB,
We have a crystal form that xtriage flags as having strong translational pseudo symmetry (Patterson peak 57% the height of the origin peak, p-value = 3E-5).
The space group is P21212. We can solve the structure with MR and refine to R=0.233 and R-free =0.276 at 2.25 Angstrom resolution. The maps look very good, but do not suggest major additional modeling that could be done to improve the structure and lower the R-factors. I know that one expects the R-factors from refinement to be higher when TPS is present, but my question is how high is too high? Has anyone done a study that shows the expectations for R-factors when TPS is present?
Thanks,
Jack
John J. Tanner Interim Chair, Department of Biochemistry Professor of Biochemistry and Chemistry Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: [email protected] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A
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