Maybe the figures were just contoured odd...but my recollection of a good 0.8 A map appearance is different....which might be consistent with the high Rf...a look at the high res data or images/stats might help?
Best, br On Mon, Feb 3, 2020, 14:58 George Sheldrick <gshe...@uni-goettingen.de> wrote: > Dear Matthias, > > > That is very strange. First please repeat the shelxl refinement with the > occupancy of the offending chlorine(s) in the .ins file changed from 11 > (i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If that > does not help I would be happy to look at it in confidence, I would need > the .hkl and .ins files. > > > Best wishes, George > > > > > On 03.02.20 12:08, Barone, Matthias 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 > > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry > University of Goettingen > Tammannstr. 4 > D37077 Goettingen > Germany > Tel: +49 551 3933021 or +49 5594 227312 > > > ------------------------------ > > 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
