Dear Hugh Morgan,
this ratio is only true if you refine your atomic model without any
geometrical restraints against the observed X-ray data. If you include
parameters for ideal geometry, you add ideal bond lengths, angles,
chiral volumes, planar groups and dihedral angles as additional
"observations". Phenix.refine reports the number of geometrical
restraints. When I look at the output of a 30 kDa protein and a 400
kDa protein, that I was recently refining, I get the following average
number of observed geometrical restraints per atom:
1.0-1.1 bond lenghts / atom
1.4 bond angles / atom
0.15 chiral volumes / atom
0.17-0.18 planar groups / atom
0.37-0.38 dihedral angles / atom
In total, these sum up to ~3.1-3.2 observed geometrical restraints/
atom. If you add these to the ~0.5 observed X-ray amplitudes/atom
(~3.6-3.7), you get a ratio observed:parameters > 1 if you refine
x,y,z (3 parameters/atom), and also >1 if you refine x,y,z,B (4
parameters/atom) with B-restraints for bonded atoms (which I count as
the same number of observed B-restraints as observed bond lengths).
If you refine instead x,y,z,grouped B-factors with 1 group per
residue, you get with 7.6-8.0 atoms per residue, approximately
0.12-0.13 parameters per atom, so 3.12-3.13 parameters/atom, and your
ratio observed:parameters is also >1.
I hope, this helps a little bit arguing with the referee.
Best regards,
Dirk.
Am 23.09.2009 um 14:48 schrieb hugh morgan:
Hi,
We are attempting to address a referees comment concerning our
data/parameter ratio for a 3.4 A structure. Although the ratio is
only 0.5, the R/Rfree is 25/29, which seems acceptable. Ideally I
would like to include a reference showing a graph or table of
data:parameter vs resolution but I have been unable to find such a
paper. Please could someone point me in the right direction.
Thanks in advance
Hugh
P.S. It would be nice to know if this table has been published
http://www-structmed.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html
or something similar to this, which includes higher resolution
structures
http://dirac.cnrs-orleans.fr/plone/Members/hinsen/data-parameter-ratio-in-x-ray-structure-determination
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Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
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