Since the Xtriage agrees with R-free, data have some issues might be
particularly at the spot identification level!What is the fraction of indexed
vs unindexed spots reported by XDS- if you run the following two lines?grep -c
" 0 0 0" SPOT.XDS # gives non-indexed spotsgrep -vc " 0 0 0" SPOT.XDS #
gives indexed spotsBest,Reza
____________________________________________
Md Rezaul (Reza) Karim, PhDScientist II, Structural Biology
On Wednesday, April 16, 2025 at 07:25:13 PM PDT, Stefan Clarke
<sclar...@fredhutch.org> wrote:
Dear CCP4 Community,
I was hoping for some insight into a problem I am having with crystal data I
collected.
The data was auto-processed with XDS to 2.1Å with the I 1 2 1 space group .
(Unit cell dimensions - 47.39, 80.131, 160.433, 90, 98.3786, 90.)
Running Xtriage in phenix showed the data likely contain translational
pseudosymmetry however, Solvent and Matthews coefficient suggests there is only
one copy of the protein complex in the asymmetric unit.
I managed to find a molecular replacement (MR) solution in phenix (using
Phaser) for the protein complex and began refinements. The electron density
map looks good and in agreement with a 2.1Å dataset. However, the refinement is
stuck with high R-work and R-free values above 0.3 suggesting there may be an
issue with the space group of the XDS auto-processed data or with the data.
I re-processed the data using both HKL2000 and XDS. Both gave C 2 2 21 as the
space group (Unit cell dimensions - 47.458, 317.576, 80.126, 90, 90, 90) and
one copy of the complex is predicted to be in the asymmetric unit. However, I
have not been able to find a MR solution with this new space group or its
enantiomers using Phaser MR in phenix.
Any suggestions and insight into this problem would be greatly appreciated. If
anything needs to be clarified, I’ll try my best to do so. Thank you in advance.
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