Hi Cedric, the PDB file reports two R/Rrfee values:
all data : 0.110 / 0.170 F>4SIG(F) : 0.103 / 0.162 while the mmCIF version has: _refine.ls_R_factor_R_work 0.103 _refine.ls_R_factor_R_free 0.134 But that R-free value doesn't seem to be present in the PDB formatted version. Also: _refine.ls_R_factor_R_work is probably the wrong item (if according to the PDB formatted version that R-value was calculated from both working and test-set reflections): shouldn't it be _refine.ls_R_factor_obs? See: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_R_factor_R_work.html Without knowing if the mmCIF was generated from a PDB formatted deposition or the other way round, it might be tricky to know what values are actually correct from just looking at the PDB archive. But looking at the paper (Table 2): Reflections with F >4 sigma (for Rfree) Isotropic: Rcryst/Rfree (%) 14.08 / 16.11 Anisotropic: Rcryst/Rfree (%) 10.29 / 13.36 All reflections (for Rfree) Anisotropic Rcryst/Rfree (%) 11.01 / 14.14 So I would say that R/Rfree = 0.110/0.141 are the 'correct' values (if Rcryst==R?). It looks like typical case of slight confusion when going from a paper to filling out the deposition form correctly. Cheers Clemens On Mon, Oct 27, 2014 at 12:00:23PM -0800, Cedric 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. > > > Thank you, > > ____________________________________________________________ > FREE ONLINE PHOTOSHARING - Share your photos online with your friends and > family! > Visit http://www.inbox.com/photosharing to find out more! -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
