Dear CCP4bb members I have a 3.0 Å dataset which has an off-origin peak of height 36% in patterson map. The peak is at fractional co-ordinates 0, 0.5, 0.5. Data has been indexed in P2(1)22(1) SG using HKL2000. I have located all the molecules in asu (as far as I know) using Molrep with the 'locked rotation' and 'Use' PST feature. After 1 round (20 cycles) of rigid body and 1 round (10 cycles) of restrained refinement (Refmac), the R and Rfree are 49 and 53 %. Although the R factors are very high, I feel the solution might be correct because the electron density follows c-alpha trace in almost all places. To be sure, I deleted a beta strand from the structure's core and repeated the refinement and found that the electron density for the strand was still present (I have no experimental phases). I have the following questions:
1) Are the final R factors never expected to reduce to acceptable values given the 36% off-origin peak? 2) What is the best way to settle the SG? I was considering P2(1)2(1)2(1), P2(1)22, P2(1)2(1)2 and P2(1)22(1), considering the off-origin peak is at 0,0.5,0.5. I found all the molecules in asu only using the P2(1)22(1) data in Molrep. Is this the best way to settle my SG? 3) Some CCP4bb archives advise either refining against weak and strong reflections alternatively (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1010&L=ccp4bb&D=0&1=ccp4bb&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=204490) or refining against medium intensity reflections. Should I also be doing these things? If yes, then what is the best way of doing it? Your suggestions and corrections to my interpretation of our data would be appreciated. Regards Shiva
