-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear DCB,
do not look at the R-values too much, look at your structure and your maps. If they look as though you cannot improve the model any further, accept that the R1/Rfree are 21% and 25% - at 1.7A resolution these values are acceptable. Go publish this structure! If you do worry, remove the ligand, refine and check if the ligand density comes back. That's a good control and probably the part of your structure you are interested in. Best, Tim On 10/12/2013 01:46 PM, Dilip Badjugar wrote: > Hello Experts, > > > I am trying to solve structure of a protein (213 a.a) complexed > with a peptide (14mer) using molecular replacement method. The > complex crystals are diffracted around 1.7 A and data is processed > in p3(2)21 space group. The structure was solved using apo protein > with good LLG -3148 and TFZ score- 49. The modeis refined in phenix > the Rfactor -26.0 and Rfree is 28.0. I have added ligand molecule > in positive density and also added water molecules (200), followed > TLS refinement but still the Rfactor not came down much ( > Rfactor-21.53 and Rfree-25.44). There no outliers in Ramachandran > plot and most of the residues (97.21) are favored region. Can you > please suggest, what can be done to reduce the Rfree? > > Thanking you in advance. DCB > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSWTxxUxlJ7aRr7hoRAiKxAJ9NEVMhxKOwagl4XkiOc/UUiPihZACfZrHx YzLCZjbw+po1Z8i2vKEHXQE= =pYsk -----END PGP SIGNATURE-----
