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 BerlinGermany
Phone: +49 (0)30 94793-284
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