Hello, it looks as though the No observations that phenix is reporting is
exactly twice the number of unique reflections. Perhaps phenix is reporting the
merging statistics for the Friedel pairs (i.e. F(+) and F(-)) within your
merged dataset. Hence the stats look much better than those for the raw data
fed to Aimless. I think you should be able to make a perfectly respectable
Table 1 with the merging stats from Mosflm/Aimless and the refinement stats
from phenix but others will know how to do it properly.
On Monday, 28 October 2019, 20:05:52 GMT, Nemanja Vuksanovic
<[email protected]> wrote:
Dear All,
I need a bit of help with an issue I am encountering with one of my datasets
when using phenix.refine. After processing data with Mosflm I get the following
parameters:
Overall InnerShell OuterShell
Low resolution limit 65.69 65.69 2.55High
resolution limit 2.45 8.83 2.45Rmerge (within
I+/I-) 0.127 0.057 0.817
Rmerge (all I+ and I-) 0.130 0.058 0.848Rmeas
(within I+/I-) 0.140 0.063 0.898Rmeas (all I+ &
I-) 0.136 0.061 0.888Rpim (within I+/I-)
0.058 0.027 0.373Rpim (all I+ & I-)
0.040 0.019 0.263Rmerge in top intensity bin
0.062 - - Total number of observations 288903 5972
32430Total number unique 25576 592
2857Mean((I)/sd(I)) 13.1 23.6
3.5Mn(I) half-set correlation CC(1/2) 0.998 0.998 0.874Completeness
100.0 99.7 100.0Multiplicity
11.3 10.1 11.4Mean(Chi^2)
1.08 0.72 0.96Anomalous completeness
100.0 99.9 100.0
Anomalous multiplicity 5.8 5.6 5.8DelAnom
correlation between half-sets -0.270 -0.466 -0.055Mid-Slope of Anom
Normal Probability 0.788 - -
After molecular replacement with PHASER and then refinement with Phenix.refine,
(defauIt settings in both) I generated a TABLE 1 in PHENIX and noticed that the
total number of observations has dropped, significantly lowering multiplicity
and R factors. Could you perhaps give me your opinion on what might be causing
this discrepancy?I'd be happy to provide the mtz file and any other information
if needed.
Table 1. Data collection and refinement statistics.
Wavelength
Resolution range 56.89 - 2.451 (2.539 - 2.451)
Space group I 2 3
Unit cell 160.9 160.9 160.9 90 90 90
Total reflections 51076 (5030)
Unique reflections 25538 (2515)
Multiplicity 2.0 (2.0)
Completeness (%) 99.96 (100.00)
Mean I/sigma(I) 13.37 (3.56)
Wilson B-factor 41.08
R-merge 0.0263 (0.1879)
R-meas 0.03719 (0.2657)
R-pim 0.0263 (0.1879)
CC1/2 0.999 (0.895)
CC* 1 (0.972)
Reflections used in refinement 25532 (2515)
Reflections used for R-free 1300 (121)
R-work 0.2698 (0.3589)
R-free 0.3115 (0.3897)
CC(work) 0.908 (0.679)
CC(free) 0.885 (0.444)
Number of non-hydrogen atoms 2310
macromolecules 2310
Protein residues 286
RMS(bonds) 0.010
RMS(angles) 1.01
Ramachandran favored (%) 96.40
Ramachandran allowed (%) 2.52
Ramachandran outliers (%) 1.08
Rotamer outliers (%) 0.00
Clashscore 8.47
Average B-factor 43.55
Best Regards,Nemanja Vuksanovic
--
Graduate StudentDepartment of Chemistry and BiochemistryUniversity of
Wisconsin-Milwaukee
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