The improvement in statistics by STARANISO is really spectacular, but I do wonder how much is caused by the directionally variable resolution limits and how much by the removal of solvent rings? The original data set statistics have big dips in CC1/2 at 6, 4.3 and 3.7 Å. Also in the final statistics table, the completeness is really high, but I guess reflections from the "bad" direction(s) are not taken into account? It would be good to also know the spherical completeness and the CC1/2 values before going too far ahead with these data. Or perhaps better phrased: I'd simultaneously try to get a dataset from a better flash-cooled crystal while trying to get the most out of this dataset.
Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) Section Editor Acta Crystallographica F https://journals.iucr.org/f/ > On 24 Oct 2022, at 03:43, Xu, Shenyuan <x...@miamioh.edu> wrote: > > Dear CCP4 community, > > I have encountered a dataset, which I thought should be easy to solve. The > volume of the cell unit seems to be expanded after image 271, which I think > is caused by radiation damage. After removing the last few images, the scaled > statistics seem good with the resolution set at 3:07 A: > > d_max d_min #obs #uniq mult. %comp <I> <I/sI> r_mrg r_meas > r_pim r_anom cc1/2 cc_ano > 91.54 8.33 3086 1197 2.58 98.44 345.2 51.3 0.101 > 0.133 0.086 0.145 0.973* -0.148 > 8.33 6.61 3005 1225 2.45 99.51 256.5 27.3 0.160 > 0.212 0.138 0.260 0.923* -0.140 > 6.61 5.78 2883 1190 2.42 98.43 92.9 9.4 0.278 > 0.368 0.237 0.461 0.541* -0.165 > 5.78 5.25 3195 1217 2.63 99.10 75.6 8.1 0.283 > 0.369 0.233 0.436 0.618* -0.107 > 5.25 4.87 3192 1206 2.65 99.42 92.5 8.3 0.281 > 0.367 0.232 0.427 0.856* -0.187 > 4.87 4.59 3230 1213 2.66 99.02 118.4 10.3 0.288 > 0.378 0.240 0.456 0.870* -0.053 > 4.59 4.36 2797 1156 2.42 92.93 137.0 12.2 0.309 > 0.410 0.266 0.496 0.843* -0.239 > 4.36 4.17 2694 1118 2.41 93.17 280.2 16.2 0.419 > 0.575 0.392 0.847 0.491* -0.142 > 4.17 4.01 3102 1188 2.61 95.50 133.6 9.9 0.392 > 0.516 0.330 0.622 0.663* -0.268 > 4.01 3.87 3224 1205 2.68 98.69 120.4 7.3 0.406 > 0.539 0.349 0.687 0.791* -0.126 > 3.87 3.75 2939 1181 2.49 98.91 90.7 6.8 0.491 > 0.652 0.425 0.810 0.691* -0.042 > 3.75 3.64 1981 1021 1.94 82.34 87.3 5.0 0.557 > 0.756 0.506 0.885 0.540* -0.018 > 3.64 3.54 2374 1082 2.19 89.13 194.6 11.2 0.502 > 0.675 0.447 0.973 0.625* -0.237 > 3.54 3.46 2622 1122 2.34 92.35 310.5 10.1 0.432 > 0.585 0.392 0.851 0.603* -0.154 > 3.46 3.38 1739 945 1.84 76.58 48.2 3.6 0.930 > 1.247 0.822 1.542 0.444* -0.046 > 3.38 3.31 2847 1240 2.30 98.57 85.4 4.2 0.691 > 0.930 0.616 1.242 0.523* -0.060 > 3.31 3.24 2838 1153 2.46 97.88 70.8 3.3 0.693 > 0.934 0.620 1.341 0.362* 0.006 > 3.24 3.18 3097 1212 2.56 97.66 71.4 2.5 0.692 > 0.924 0.605 1.173 0.526* 0.044 > 3.18 3.12 3204 1216 2.63 99.10 79.6 3.7 0.668 > 0.886 0.576 1.338 0.440* -0.081 > 3.12 3.07 3059 1172 2.61 98.16 73.5 2.4 0.714 > 0.945 0.612 1.633 0.362* -0.177 > 91.50 3.07 57108 23259 2.46 95.22 138.4 10.8 0.383 > 0.513 0.336 0.671 0.656* -0.149 > > I used Mrbump to do the MR, most sequence identities of the starting > templates are more than 0.85, and some of them are structures predicted from > alpha fold 2. But after refinement (including jelly-body, proSmart, TLC), the > best R/Free R stuck at around 0.42/0.45. Inspecting the electron density map > shows that the model does not fit the electron density well. The space group > is P1, Cell is 58.49 63.97 91.60 91.71 91.86 99.47, should be 5 or 6 > molecules in the asymmetric unit. > > I checked the data quality, it said the data is highly anisotropy. Then > I searched the CCP4 forum and used the STARANISO Server and UCLA server, but > still cannot improve the refinement. The data statistics after drawing > ellipsoidal resolution limits is good: > > <pre> > resolution observed redundancy completenes rmerge > i/sigma > before/after before/after before/after before/after > before/after > 7.90 4957 1185 3.5 3.3 97.3% 92.6% 13.0% 12.7% 11.9 > 7.2 > 5.58 8023 2397 3.0 3.6 98.6% 98.9% 30.3% 11.8% 5.5 > 7.5 > 4.56 11176 2624 3.3 3.1 99.1% 97.5% 57.1% 18.2% 3.7 > 6.3 > 3.95 11694 3213 2.9 3.1 94.0% 99.0% 53.1% 27.5% 4.2 > 4.3 > 3.53 12065 3524 2.6 3.0 92.8% 99.0% 49.8% 45.9% 3.2 > 2.8 > 3.22 12828 4098 2.5 3.2 93.8% 99.1% 69.3% 53.2% 2.1 > 2.7 > 2.98 17566 4628 3.2 3.3 98.6% 99.1% 98.1% 60.0% 1.6 > 2.7 > 2.79 19405 4631 3.3 3.1 98.1% 96.8% 203.0% 70.3% 0.8 > 2.7 > 2.63 20871 4001 3.3 2.5 98.1% 90.1% 760.1% 41.2% 0.3 > 3.4 > 2.50 20352 5406 3.0 3.2 97.8% 97.3% -99.9% 66.0% 0.0 > 2.6 > 2.38 17281 5689 2.5 3.2 93.8% 98.2% -99.9% 81.4% 0.0 > 1.8 > 2.28 13198 3874 1.8 2.1 68.6% 88.0% 546.3% 193.2% 0.1 > 0.6 > 2.19 10429 4961 1.4 2.6 52.5% 92.7% -99.9% 31.0% 0.0 > 4.8 > 2.11 7776 4275 1.0 2.1 41.2% 90.1% -99.9% 266.0% 0.0 > 0.6 > 2.04 5561 6084 0.7 2.9 30.9% 97.6% 531.4% 109.2% 0.1 > 1.1 > 1.97 3818 6700 0.4 3.1 23.4% 97.4% -99.9% 85.8% 0.0 > 1.6 > 1.91 2269 5906 0.3 2.7 17.0% 83.9% -99.9% 87.3% 0.0 > 1.5 > 1.86 1191 5250 0.1 2.3 10.4% 69.2% -99.9% 167.5% 0.0 > 0.9 > 1.81 433 3961 0.0 1.7 4.5% 51.0% -99.9% 225.7% 0.0 > 0.8 > 1.77 60 2168 0.0 0.9 0.6% 27.2% -99.9% 254.0% 0.0 > 0.7 > total 200953 84575 1.6 2.6 54.7% 84.6% 78.6% 54.0% 1.4 > 2.4 > </pre> > > Any suggestions would help. I can provide the collected image dataset and the > sequence if anyone is interested. > > Thanks, > > Shenyuan Xu > Miami University > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
