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 isstuck 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 andupdated 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
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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry
University of Goettingen
Tammannstr. 4
D37077 Goettingen
Germany
Tel: +49 551 3933021 or +49 5594 227312
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