-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear S. M. Jaimohan,
one reason such a discrepancy is often the presence of TLS, which may be present in the PDB-header but is not found in the PDB coordinates. Another reason might be that during deposition |F| and I got confused - - this is not too uncommon for elderly entries. A more up-to-date reason is that programs calculate R values very differently. If you take a PDB file refined with program X and put it into program Y you easily get discrepancies greater than 5%. At the DGK meeting two weeks ago some structures were presented solved at 3'ish A resolution with R/Rfree near 14%/16%, which I would be very suspicious about... That's why I think that R-values are becoming meaningless. They are useful guides for the refinement of one particular structure with one particular program, but any deviation from this and you cannot compare R-values. Other validation tools like those implemented in Coot or the Molprobity server are much more reliable. Maybe that's a good thing because this makes people move away from using a single number to judge about 10,000s of parameters. Best, Tim On 04/04/2014 10:07 AM, jai mohan wrote: > Dear all, Sorry for the off-topic Question. I just tried to extract > files *.* from EDS server for a PDB entry. The page tells us that > > There is no map available for this entry (****), because our > automatic script failed to produce an electron density map with an > R-value (0.309) within 5 percentage points of the published one > (0.165). If you are the author of this entry and wish to help us > remedy this situation, please contact us. Back to EDS home page > > > The reported R-value for the (****) PDB entry is 0.16 than how > 0.309? could anyone please explain about this! > > Sincerely, S.M. Jaimohan, Ph. D > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BE -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTPnQBUxlJ7aRr7hoRAoNVAJ9eSKs+Zq5dz1cryZB/8qC+FtnleQCfamDY UPpJZTTMIRPqGrS+YpDVq+0= =DuKK -----END PGP SIGNATURE-----
