[phenixbb] on the Crystallographic data and refinement statistics table in the crystallography paper
sebastiano.pasqualato at gmail.com
Mon Apr 30 01:12:42 PDT 2012
I just wanted to let you know that when processing the data with XDS (in my case with xia2) and providing the CORRECT.LP logfile to phenix.table_one, the program fails to extract information on total reflections, multiplicity, Rsym.
I have a question, too.
In the case the refinement resolution is different from the integration one, would the table give both series of values.
I usually put in table 1 also the reflections not used in refinement (i.e. the Rfree set number of reflections). Would be nice to have it there.
Thanks a lot,
Resolution range (Å) 43.85 - 3.01 (3.118 - 3.01)
Space group C 1 2 1
Unit cell 175.42 41.52 107.52 90 90.88 90
Unique reflections 15744 (1536)
Completeness (%) 99.38 (99.81)
Mean I/sigma(I) 7.62 (2.43)
Wilson B-factor 50.95
R-factor 0.2039 (0.3125)
R-free 0.2570 (0.4131)
Number of atoms 3729
Protein residues 452
Ramachandran favored (%) 89
Ramachandran outliers (%) 3.6
Average B-factor 67.50
On Apr 26, 2012, at 2:22 PM, Nathaniel Echols wrote:
> On Thu, Apr 26, 2012 at 6:57 AM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
>> In the protein crystalographic paper, there is always a table on
>> Crystallographic data and refinement statistics. Do you have some
>> suggestions on which items should be contained in this item?
> Yes, run phenix.table_one (I recommend using the GUI in the latest
> nightly build for this), supplying it your model, data, and
> integration/scaling log files, and it will generate a table that
> should be suitable for most journals.
> Many journals also have their own recommendations; check the author
> instructions for either NSMB, Structure, or Acta D, you should find
> some kind of template. (I cribbed from these when writing the
> program; they're all pretty similar, with minor differences.)
> phenixbb mailing list
> phenixbb at phenix-online.org
Sebastiano Pasqualato, PhD
Department of Experimental Oncology
European Institute of Oncology
via Adamello, 16
20139 - Milano
tel +39 02 9437 5167
fax +39 02 9437 5990
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