Hello,
I am trying to solve an X-ray structure of a protein of which the structure is already known. My aim is to only seek for ligands (soaking) and interpret any conformational changes. Since I am using a model with 100% sequence identity from PDB I am not doing Autobuild after Molecular phasing and continue directly with phenix.refine according to reccomendations (10 rounds). In accordance with X-triage I am also using NCS default settings in the refinement. This refinement produces solid R free and R work values around 0.29 and 0.22. The problem becomes when I want to manually edit the structure, correct the loops which are changed upon binding of the ligand, and correct any outliers. This results in R free slightly lower than R work. Upon refining, R work drops normally while R free rises significantly (for 0.2 -0.3). I have been trying to crack this for a few days with no success. I read that slightly lower R free can be normal in such cases but nevertheless both R values should drop, and haven’t found anything about the big rise of this value after refinement. It feels like I am missing something, since this is my first time solving a structure. Any advice? Thank you, Nika ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
