Hi Matthias, did you use correct model parameterization and optimal refinement strategy for the resolution? Such as: - Add H atoms; - Refine all but H atoms with anisotropic ADPs; - Model alternative conformations (that one'd expect many at this resolution); - Add solvent (water, crystallization cocktail components if you see any); - Relax restraints on geometry and ADPs; .... long list!
If not, then what you have in terms of R factors is more or less what I'd expect. In the absence of obvious data pathologies, I'd expect Rwork/Rfree in 10-15% range, and the Rfree-Rwork gap around 1-2% or less. Since you mentioned Phenix refinement, I am happy to help you with details etc off-list. Pavel On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias <bar...@fmp-berlin.de> wrote: > Dear ccp4 community > > Im having some problems solving a 0.73A structure. Spacegroup seems to be > correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer > shell CC1/2 24% and 90.4% complete. > > The model is nearly fully built, there is no remaining unmodelled areas. > However, Rfact is stuck 27% in phenix, with a very distinct artifact in > the electron map (see phenix.jpg). You can see difference density on > various well defined sidechain atoms. Notably, they seem to follow a > pattern: Nearly all Val CG have difference signal, as well as many backbone > NH. Hence, I suspected that it might be a problem with the SF, since we > recorded the DS at 0.86A. > > > Hence I gave shelxl a shot: > > I used the refined model from phenix, converted it via pdb2ins and pasted > the restraints created by prodrg. > > The shelxl hkl was produced by xdsconv, using the freeR flagging of the > mtz used by phenix (no merge, friedel false). > > Interestingly, shelxl can bring Rfree down to 16% and almost all of > the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg). > Except one: the inhibitor contains a chlorinated phenylring (pdb ligand > 2L5) which now shows massive difference density for Cl. > > I therefore suggested that I might deal with a wrong SF for Cl. Funny > enough, pdb2ins does not produce a DISP line for Cl if converting the pdb > that contains the inhibitor. Hence, I used pdb2ins and the pdb from > PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line > > DISP $CL 0.18845 0.21747 1035.16450 > > into the .res file and updated the UNIT line. Shelxl runs through, and > the density looks ok on the Chloride now. However Rfree is back up at 24% > and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): > now, very distincitvly, backbone carbonyls and NHs show difference density. > > Am I right in my assumption, that the SFAC of Cloride is not properly > calculated at the given wavelenght? And if so, how do I guess it correctly? > > > Thank you very much for your help! > > Best, matthias > > > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
