Dear all, I have two questions. I would like to find out the community consensus of (1) best practices in refining against lower resolution data (~4 angstrom) to achieve the best model, and also (2) what manuscript referees should ask for in this regard. One might encounter a hypothetical situation where standard refinement approaches gave a model with poor Ramachandran statistics. Imposing Ramachandran restraints gave a model with improved Ramachandran statistics but at the expense of higher Rfree. I would expect that the model with better geometry is probably more reliable, and wonder if this is the general consensus view? I also wonder should a referee be the geometry police, or should authors/depositors have discretion to submit/publish the model they prefer so long as refinement protocol is accurately described and weaknesses such as poor Ramachandran statistics are evident in the presentation of the data and not concealed?
Thanks for your input! Evette Evette S. Radisky, Ph.D. Associate Professor and Consultant Department of Cancer Biology Mayo Clinic Cancer Center _________________________________________ Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 http://www.mayo.edu/research/faculty/radisky-evette-s-ph-d/bio-00094471
