On Thu, 8 May 2014 16:56:01 +0200, Christophe Wirth <[log in to unmask]> wrote:
>Dear all,
>
>To add another bit to the discussion, I would say that an increase of Rmerge and Rmeas is just expected in such a case, isn't it?
>
>According to your tables, in P1, the multiplicity is about 4. In P2, it's about 7. In P3, it's 10. And in P6, it's approaching 20. I would say that this leads us to the now "classical" problem those statistics have with high multiplicity datasets.
Rmeas does not have this problem, only Rmerge has it!
But there are other factors which produce higher (and more realistic!) Rmeas in the higher-symmetry spacegroup, like radiation damage and absorption or other systematic differences that can not be removed by scaling.
In other words: in an ideal experiment Rmeas should be the same for the correct space group and its sub-groups. In a real experiment, however, Rmeas in a high-symmetry space group "sees" the differences resulting from systematic errors, whereas Rmeas in a low-symmetry space group often does not "see" it - simply because it does not compare those reflections which suffer from the error.
best,
Kay
>
>Best,
>
>Christophe
>
>
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>
>----------------------------------------------------------
>Christophe Wirth, PhD
>Centre for Biological Signalling Studies (bioss)
>Institute for Biochemistry and Molecular Biology
>University of Freiburg
>Stefan-Meier-Str. 17
>D-79104 Freiburg, Germany
>Tel: +49 (0) 761 203 52 77
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>-----Ursprüngliche Nachricht-----
>Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von <Rain Field>
>Gesendet: Mittwoch, 7. Mai 2014 19:26
>An: [log in to unmask]
>Betreff: [ccp4bb] Space group problem
>
>Hi all,
>I have a 360 degree data set collect on home beam.
>I used XDS to integrate the frames in P1.
>I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the log below.
>The cell looks like P3 and pointless suggest P6. But the Rmerge and Rmeas are much higher than normal at I/sigmaI=2.
>I think P1 might be the true space group. But the Rpim reported by aimless seems high in the high resolution shell. Why is that?
>Thanks!
>
> LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) REINDEXING TRANSFORMATION
> CHARACTER LATTICE OF FIT a b c alpha beta gamma
>
> * 31 aP 0.0 62.5 82.5 82.6 60.1 89.9 90.0 -1 0 0 0 0 -1 -1 0 0 -1 0 0
> * 44 aP 0.2 62.5 82.5 82.6 119.9 90.1 90.0 1 0 0 0 0 1 1 0 0 -1 0 0
> * 41 mC 0.6 143.1 82.5 62.5 90.0 90.1 90.0 0 1 -1 0 0 -1 -1 0 -1 0 0 0
> * 30 mC 0.7 82.5 143.1 62.5 89.9 90.0 90.0 0 -1 -1 0 0 1 -1 0 1 0 0 0
> * 35 mP 1.0 82.5 62.5 82.6 90.1 119.9 90.0 0 -1 -1 0 -1 0 0 0 0 1 0 0
> * 40 oC 1.2 82.5 143.1 62.5 89.9 90.0 90.0 0 -1 -1 0 0 -1 1 0 -1 0 0 0
> * 20 mC 2.6 142.9 82.6 62.5 90.0 90.0 90.1 0 -2 -1 0 0 0 -1 0 1 0 0 0
> * 23 oC 3.3 82.6 142.9 62.5 90.0 90.0 89.9 0 0 1 0 0 -2 -1 0 1 0 0 0
> * 25 mC 3.3 82.6 142.9 62.5 90.0 90.0 89.9 0 0 1 0 0 -2 -1 0 1 0 0 0
> * 22 hP 3.5 82.5 82.6 62.5 90.1 90.0 119.9 0 1 1 0 0 -1 0 0 1 0 0 0
> 37 mC 249.8 176.5 62.5 82.5 90.0 117.8 69.3 1 -2 0 0 1 0 0 0 0 1 1 0
> 42 oI 250.0 62.5 82.5 156.1 90.0 113.6 90.0 -1 0 0 0 0 -1 -1 0 1 -1 1 0
> 39 mC 250.6 176.4 62.5 82.6 90.0 117.9 69.2 1 -2 -2 0 1 0 0 0 0 0 1 0
> 33 mP 434.8 62.5 82.5 82.6 119.9 90.1 90.0 1 0 0 0 0 1 1 0 0 -1 0 0
> 34 mP 435.2 62.5 82.6 82.5 119.9 90.0 90.1 -1 0 0 0 0 1 0 0 0 -1 -1 0
> 32 oP 435.4 62.5 82.5 82.6 119.9 90.1 90.0 1 0 0 0 0 1 1 0 0 -1 0 0
> 21 tP 437.6 82.5 82.6 62.5 90.1 90.0 119.9 0 1 1 0 0 -1 0 0 1 0 0 0
>
>
>
>P1:
> SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
>
> 8.45 4500 1165 1288 90.5% 2.2% 2.4% 4498 51.19 2.6% 99.9* 10 0.838 1030
> 6.27 7174 1844 1872 98.5% 3.1% 3.0% 7173 35.92 3.6% 99.9* 11* 0.906 1671
> 5.20 9009 2288 2324 98.5% 4.5% 4.3% 9008 26.88 5.2% 99.8* 4 0.835 2168
> 4.55 10597 2686 2744 97.9% 5.2% 5.2% 10595 22.65 6.0% 99.7* -2 0.776 2557
> 4.09 12051 3051 3147 96.9% 7.5% 7.5% 12048 16.93 8.7% 99.4* 2 0.779 2915
> 3.75 12740 3226 3342 96.5% 14.8% 14.5% 12738 9.37 17.1% 98.2* 1 0.760 3078
> 3.48 14344 3631 3738 97.1% 22.2% 22.2% 14342 6.36 25.7% 95.8* 0 0.785 3471
> 3.26 15079 3813 3948 96.6% 47.3% 48.5% 15076 2.99 54.8% 83.7* -1 0.714 3655
> 3.08 14088 3797 4242 89.5% 99.7% 105.6% 13945 1.30 116.0% 58.6* -2 0.636 3133
> total 99582 25501 26645 95.7% 7.7% 7.9% 99423 14.49 9.0% 99.9* 1 0.765 23678
>
>P2:
> SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
>
> 8.45 4499 638 711 89.7% 2.5% 2.7% 4497 63.58 2.8% 100.0* 16* 0.892 534
> 6.27 7172 986 993 99.3% 3.5% 3.5% 7172 46.06 3.7% 99.9* 10 0.948 872
> 5.20 8963 1202 1213 99.1% 4.9% 4.9% 8963 35.19 5.3% 99.9* 2 0.849 1101
> 4.55 10598 1413 1427 99.0% 5.8% 5.9% 10598 29.79 6.2% 99.9* -5 0.781 1308
> 4.09 12047 1608 1630 98.7% 8.5% 8.4% 12047 22.42 9.1% 99.6* -7 0.758 1500
> 3.75 12672 1687 1721 98.0% 16.2% 16.0% 12672 12.64 17.4% 98.9* 0 0.753 1591
> 3.48 14380 1918 1925 99.6% 24.7% 24.5% 14380 8.50 26.5% 97.9* -1 0.806 1806
> 3.26 15077 2011 2024 99.4% 51.5% 53.6% 15077 4.05 55.4% 90.8* -2 0.713 1907
> 3.08 14130 2055 2169 94.7% 109.3% 117.3% 14076 1.71 118.1% 73.6* -4 0.624 1799
> total 99538 13518 13813 97.9% 8.6% 8.8% 99482 18.92 9.2% 99.9* -2 0.768 12418
>
>P3:
> SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
>
> 8.45 4507 394 429 91.8% 2.8% 3.0% 4506 78.31 2.9% 100.0* 22* 0.920 393
> 6.27 7171 621 621 100.0% 3.8% 3.7% 7171 56.42 3.9% 100.0* 19* 1.021 621
> 5.20 8953 769 774 99.4% 5.2% 5.1% 8953 43.07 5.4% 99.9* 4 0.886 769
> 4.55 10586 907 911 99.6% 6.1% 6.2% 10586 36.58 6.4% 99.9* -1 0.774 907
> 4.09 11997 1033 1045 98.9% 8.9% 8.8% 11997 27.69 9.3% 99.8* -2 0.768 1033
> 3.75 12620 1087 1112 97.8% 16.8% 16.6% 12620 15.75 17.5% 99.4* 0 0.777 1087
> 3.48 14358 1240 1240 100.0% 25.7% 25.6% 14358 10.50 26.9% 98.5* -4 0.776 1240
> 3.26 15023 1302 1306 99.7% 52.5% 55.0% 15023 5.11 54.9% 94.1* 1 0.718 1301
> 3.08 14198 1358 1410 96.3% 113.0% 122.5% 14162 2.12 118.7% 79.3* -7 0.617 1263
> total 99413 8711 8848 98.5% 9.0% 9.2% 99376 23.01 9.4% 100.0* 0 0.777 8614
>
>P1(aimless)
> Overall InnerShell OuterShell
>Low resolution limit 19.82 19.82 3.46
>High resolution limit 3.20 8.47 3.20
>Rmerge (all I+ and I-) 0.071 0.022 0.561
>Rmeas (all I+ & I-) 0.082 0.026 0.649
>Rpim (all I+ & I-) 0.041 0.013 0.326
>Total number of observations 90529 4500 18945
>Total number unique 22976 1165 4789
>Mean((I)/sd(I)) 16.1 53.6 2.5
>Mn(I) half-set correlation CC(1/2) 0.999 0.999 0.806
>Completeness 97.6 91.4 97.0
>Multiplicity 3.9 3.9 4.0
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