Dear Appu, Did you try to run phaser in C222 as well? Your space group is most likely C2221 as pointless and xtriage suggest, but the space group might be different, especially if the 2 molecules in the a.u. are related via some pseudo crystallographic symmetry. Also, some additional runs of Phaser do not take a huge effort. High R and Rfree’s with reasonable electron density may occur of one of the molecules is correctly positioned, and the other has the correct orientation, but is translated.
Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Appu kumar Gesendet: Mittwoch, 22. April 2015 23:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Refinement at 4A resolution Dear CCP4 Member, I seek your advice on the refinement issues at the low resolution 4A. I am trying to refine a membrane protein structure after getting the phases from MR using the PHASER. The soluble domain structure which comprises of 40% of protein has been used as template (sequence identity 80%) in MR search . The PHASER gave a good solution having TFZ value of about 14.3. I have then created the polyA model for the transmembrane domain from distant homolog which share 30% sequence identity for TM region and try to find the phases for whole TM domain keeping the soluble domain fixed. I got lucky in getting the phases for the whole protein using the PHASER (TFZ=17.6) but the during the refinement, Rwork and Rfree got stalled at the 41 and 44 respectively after several cycle of the refinement in both refmac and phenix. I checked the spacegroup with pointless and it suggests C2221. I have attached the pointless and phenix.xtriage run file with this mail for your evaluation. Phenix.xtriage suggests no major pathologies with the data except the mild psuedomerohedral twining. There are two molecules of protein in ASU. Evaluation of the density maps, suggest reasonable map for the most of protein part. I am wondering why Rwork and Rfree are not coming down despite of the good MR solution and what i am doing wrong with refinement and if there is some pathologies associated with the data which needs to be answered before heading to refinement. Thanks for your help in advance. Appu
