Dear all, I am currently trying to refine co-crystallized ligand structures at 2.8-3.4 Å resolution. After initial molecular replacement the density in the maps, both 2Fo-Fc and Fo-Fc looks good and the ligand seams to have bound. However after running Refmac directly on the output files the maps get much worse. I am using a "clean" pdb, without ligand or water for the Phaser and subsequent Refmac runs. Also when refining with the ligand in the B factors are a lot higher for the ligand then the surrounding residues, only when lowering the occupancy to 0.7-0.8 for the ligand the B factors look better. Is that acceptable to do at this resolution? R-free is in the 0.24-0.27 range. There is only a marginal change in R-free with the addition of ligand. TLS refinement seams to help alot for overall R values but does not improve the maps. I have also tried Phenix with simulated annealing, rigid body and reference structures. So the question is how best to proceed with refinement at the rather low resolution??
Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: [email protected] phone: 0046 8 524 876 33 fax: 0046 8 736 04 39
