On Thu, 8 May 2014 16:56:01 +0200, Christophe Wirth <christophe.wi...@biochemie.uni-freiburg.de> 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 > > > > >---------------------------------------------------------- >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 >---------------------------------------------------------- > > > > > > > > > > > > > > >-----Ursprüngliche Nachricht----- >Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von <Rain >Field> >Gesendet: Mittwoch, 7. Mai 2014 19:26 >An: CCP4BB@JISCMAIL.AC.UK >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
