To add to the current anisotropic discussion I recently got a dataset I’m
unable to refine and I’m hoping I could get some help on figuring out if
there’s anything I can do.
I get a clear cut solution with Phaser using the same protein as search model
and got a TFZ of >16, LLG >200, and a packing that makes sense, so I don’t
doubt the solution. However, the maps look terrible, more like something I
would expect from a 3.65Å dataset rather than the 2.65Å it supposedly is.
The dataset merges well in I4122 to 2.65Å with an overall Rmerge of 5% and a
CC1/2 of >0.5 in the outer shell (see the bottom for full summary). There is
some minor radiation damage but I could cut out most of it due to the high
symmetry.
Xtriage reports no indication of twinning, but does say that the data is
moderately anisotropic, so I ran the unmerged data through the StarAniso
server, which reported the ellipsoidal resolution limits to be 2.304, 2.893,
and 3.039. Refining with the anisotropically truncated data improves the maps
somewhat, but I am still unable to get the Rfree below 38%. I tried using both
phenix.refine and buster with similar results.
I’ve considered the choice of space group and tried I41, F222, I212121 , and
C2, but with the same results, and Zanuda tells me the same thing.
Lastly, there is some minor ice rings, so my last try was to exclud the ice
ring resolutions, but this made little to no difference.
Normally I would just write this off as the data being bad but this time all
the statistics tell me this should be doable so I’m curious what has gone wrong.
Cheers
Michael Jarva
Summary data for Project: XDSproject Crystal: XDScrystal Dataset:
XDSdataset
Overall InnerShell OuterShell
Low resolution limit 34.87 34.87 2.78
High resolution limit 2.65 8.79 2.65
Rmerge (within I+/I-) 0.052 0.026 1.595
Rmerge (all I+ and I-) 0.057 0.030 1.805
Rmeas (within I+/I-) 0.062 0.031 1.924
Rmeas (all I+ & I-) 0.063 0.033 1.993
Rpim (within I+/I-) 0.032 0.017 1.042
Rpim (all I+ & I-) 0.025 0.014 0.817
Rmerge in top intensity bin 0.030 - -
Total number of observations 19931 566 2681
Total number unique 3597 114 471
Mean((I)/sd(I)) 11.3 42.3 0.8
Mn(I) half-set correlation CC(1/2) 0.999 0.999 0.575
Completeness 97.9 93.1 99.6
Multiplicity 5.5 5.0 5.7
Anomalous completeness 92.4 92.1 96.8
Anomalous multiplicity 3.0 3.0 3.0
DelAnom correlation between half-sets 0.176 0.258 0.051
Mid-Slope of Anom Normal Probability 1.078 - -
Average unit cell: 82.39 82.39 69.73 90.00 90.00 90.00
Space group: I 41 2 2
Average mosaicity: 0.10
