From: Ta Hai Sent: Sat 7/26/2008 3:00 AM To: Sampath Natarajan Subject: RE: [ccp4bb] Refinement problem
With the R and freeR factor 45.3% and 51.4%, I'm quite sure that your MR solution is not correct. Although your current model seems fitting with the map, but it's just the biased map after refinement with REFMAC. While now you can't be sure that whether your crystal contain Se atom or not, try MR again: - Make sure you estimate correctly the numbers of molecules/AU. - Prepare the best search model as much as you can - Try with different programs like Molrep, EPMR, Phaser... Good luck, Hai ________________________________ From: CCP4 bulletin board on behalf of Sampath Natarajan Sent: Sat 7/26/2008 2:05 AM To: [email protected] Subject: [ccp4bb] Refinement problem Dear all, Now I'm solving a structure with 1.6A resolution. The data seems good with R-sym (12.4) and all other parameters. Actually the data was collected with SAD phasing. When we checked the data we couldn't find the Se atom in the structure. Since the data resolution is good, we tried to do molecular replacement using Balbes program. It was selected a model with 25% sequence identity and we got the good solution too. I could find all residues in the density and also checked the Ramachandran map which shows almost all residues are in the allowed region. The problem is, I have done refinement many times, the R-factor (45.3) and R-free (51.4) is not reducing during the refinement and also figure of merit is not increasing. Still it remains what I got during the first refinement. The density is also not improving much. Also I could find many cuts in the density. My question is........ 1. Can we use SAD phasing data for MR solution? 2. Is there any other way to reduce the R/R-free? 3. Why the figure of merit is not increasing even after modeled the residues exactly into the electron density? Thanks, Regards, Sampath
