Re: [phenixbb] on the Crystallographic data and refinement statistics table in the crystallography paper

30 Apr 2012

      HI Nat,

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,
ciao,
s

                                                  Refine16
          Wavelength (Å)                                 
    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
        Total reflections                                 
       Unique reflections                     15744 (1536)
             Multiplicity                                 
         Completeness (%)                    99.38 (99.81)
          Mean I/sigma(I)                      7.62 (2.43)
          Wilson B-factor                            50.95
                    R-sym                                 
                 R-factor                  0.2039 (0.3125)
                   R-free                  0.2570 (0.4131)
          Number of atoms                             3729
           macromolecules                             3702
                  ligands                                 
                    water                               27
         Protein residues                              452
               RMS(bonds)                            0.006
              RMS(angles)                             1.19
 Ramachandran favored (%)                               89
Ramachandran outliers (%)                              3.6
               Clashscore                            22.85
         Average B-factor                            67.50
           macromolecules                            67.70
                  solvent                            33.10

On Apr 26, 2012, at 2:22 PM, Nathaniel Echols wrote:
...
On Thu, Apr 26, 2012 at 6:57 AM, Dialing Pretty  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.)
-Nat
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Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
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