[phenixbb] R/R free reported values

Tim Gruene tg at shelx.uni-ac.gwdg.de
Tue Oct 28 01:46:29 PDT 2014

Hi Phil,

SHELXL does make no difference between structure types, and it always
reports both values. I ignore the cut-off value, though.

Differences are usually due to solvent models, and the less solvent in
the structure the less differences you'd expect.
In this case, though, I assume a type in the
_pdbx_refine.free_R_factor_no_cutoff rather than anything else.

The structure is from 2005, when much manual work was necessary for
structure deposition.


On 10/27/2014 09:48 PM, Phil Jeffrey wrote:
> I believe SHELXL reports R1 cut at 4 sigma F and also R1 on all data,
> which I've got to bet is the source of those two different values.
> However I've never used SHELXL for protein and don't know if the cutoff
> is redefined for protein data.
> (R1 = R-factor on F).
> Phil Jeffrey
> Princeton
> On 10/27/14 4:13 PM, Nathaniel Echols wrote:
>> I don't have an exact explanation, but there is some inconsistency in
>> the way data are stored internally by the PDB.  The mmCIF file is the
>> most complete representation:
>> _refine.ls_R_factor_R_work                     0.103
>> _refine.ls_R_factor_R_free                     0.134
>> ...
>> _pdbx_refine.R_factor_all_no_cutoff                      0.1101
>> _pdbx_refine.R_factor_obs_no_cutoff                      ?
>> _pdbx_refine.free_R_factor_no_cutoff                     0.1704
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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