On Mon, Oct 27, 2014 at 1:00 PM, Cedric <patrick.cossins@inbox.com> wrote:

Hi Phenix and CCP4 community,

(sorry for the cross posting).

I was looking at a PDB file.

The http://www.rcsb.org/ website page gives the following values:

R-Value: 0.103 (work)
R-Free:  0.134

The actual PDB file gives the following:

R :0.110
FREE R VALUE : 0.170

I was wondering why the difference. The structure is 1.0A resolution 2CWS.

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

So, the first set is what gets displayed on the web page, the second set ends up in the PDB header.  I suspect something went awry in deposition, but only the PDB and the depositors can answer that question.

I wouldn't take the advertised statistics at face value anyway; I prefer to rely on recalculated values (and if these are significantly different, I view the structure with suspicion).  In this case, phenix.model_vs_data says:

    r_work(re-computed)                : 0.1081 

    r_free(re-computed)                : 0.1377 

which, accounting for the precision loss in PDB format and the differences between SHELXL and Phenix, are reasonable enough, and suggest that the values on the web page are probably accurate.

-Nat

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