Are you sure you have identified the correct space group? Cheers
Schara Dr. Schara Safarian Project Leader Max Planck Institute of Biophysics Department of Molecular Membrane Biology Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland/Germany Visiting Assistant Professor University of Otago Department of Biochemistry & Microbiology Dunedin/New Zealand Twitter <https://twitter.com/SafarianSchara> Google Scholar <https://scholar.google.com/citations?hl=de&user=SjePlggAAAAJ> > Am 02.11.2020 um 11:26 schrieb Nika Žibrat <nika.zib...@ki.si>: > > > 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 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## 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/
