WORK-IN-PROGRESS
1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2 Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Wiersum, G., Godzik, A., Jaroszewski, L., Stogios, P.J., Skarina, T., Satchell, K.J.F. To be published.
Data was collected on 7th March 2020 on beamline 21-ID-F (LS-CAT, APS) on a Rayonix MX-300 CCD detector and refined to 1.8A.
There are 200 images of 0.6 degree/image, i.e. 120 degrees of data. But we have to be careful: the last 5 images are currupted and should be excluded:
| 195 | 196 | 197 | 198 | 199 | 200 |
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Running
process -Id A,Images,idp51000-201-a_1_2_3.###,1,195gives us
Spacegroup name P3121
Unit cell parameters 167.722 167.722 51.941 90.0 90.0 120.0
Wavelength 0.97872 A
Diffraction limits & principal axes of ellipsoid fitted to diffraction cut-off surface:
1.756 1.0000 0.0000 0.0000 0.894 _a_* - 0.447 _b_*
1.756 0.0000 1.0000 0.0000 _b_*
1.677 0.0000 0.0000 1.0000 _c_*
Criteria used in determination of diffraction limits:
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local(I/sigI) >= 1.20
Overall InnerShell OuterShell
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Low resolution limit 54.900 54.900 1.780
High resolution limit 1.701 4.832 1.701
Rmerge (all I+ & I-) 0.055 0.031 1.147
Rmeas (all I+ & I-) 0.059 0.033 1.238
Rpim (all I+ & I-) 0.022 0.012 0.463
Total number of observations 608799 28937 28754
Total number unique 83442 4172 4175
Mean(I)/sd(I) 17.6 47.9 1.4
Completeness (spherical) 90.8 99.9 35.7
Completeness (ellipsoidal) 95.4 99.9 56.0
Multiplicity 7.3 6.9 6.9
CC(1/2) 0.999 0.999 0.596
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The data has high enough multiplicity to also allow computation of radiation-damage detection maps F(early)–F(late):
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Files:
Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2. Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) To be published.
Data was collected on 10th March 2020 on beamline 19-ID (SBC-CAT, APS) on a Pilatus3 6M and refined to 2.00 A using Phenix.
There is a whole collection of different sweeps (using autoPROC's find_images tool):
m4G4eg_#####.cbf : 1 - 54
m4G4eg-2_#####.cbf : 1 - 237
m4G4eg-3_#####.cbf : 6 - 160
m4G4eg-3_#####.cbf : 166 - 180
m4G4eg-4_#####.cbf : 50 - 156
m4G4eg-5_#####.cbf : 25 - 90
with between 50 and 100 seconds gap between them. There seems to be some images missing from the deposited data?
All were collected at the same distance, wavelength and using the same oscillation angle (0.5 deg/image) and exposure time (0.5 sec/image).
The same caveats/questions as for 6W9C can be applied here: this is high-dose, low-multiplicity wide-sliced data when ideally we would like to see low-dose, high-multiplicity fine-sliced data collected on a low-noise pixel-array detector using shutterless data collection. It would be interesting to find out why those parameters are different in all three aspects to the typical approach for collecting the best data on those modern instruments.
We can run autoPROC using
process -I Images ReverseRotationAxis=yes -d 01 | tee 01.lis
which will process each sweep separately and automatically scale and merge all six together at the end to give:
Spacegroup name P3121
Unit cell parameters 168.5282 168.5282 51.9549 90.0 90.0 120.0
Wavelength 0.97918 A
Diffraction limits & principal axes of ellipsoid fitted to diffraction cut-off surface:
1.970 1.0000 0.0000 0.0000 0.894 _a_* - 0.447 _b_*
1.970 0.0000 1.0000 0.0000 _b_*
1.909 0.0000 0.0000 1.0000 _c_*
Number of RUNs (sweeps) contributing to this dataset = 5
Criteria used in determination of diffraction limits:
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local(I/sigI) >= 1.20
Overall InnerShell OuterShell
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Low resolution limit 48.946 48.946 2.009
High resolution limit 1.923 5.226 1.923
Rmerge (all I+ & I-) 0.160 0.062 6.190
Rmeas (all I+ & I-) 0.165 0.064 6.372
Rpim (all I+ & I-) 0.039 0.016 1.506
Total number of observations 1040750 56010 47339
Total number unique 58835 3336 2671
Mean(I)/sd(I) 16.5 49.2 1.3
Completeness (spherical) 91.5 100.0 34.1
Completeness (ellipsoidal) 95.2 100.0 49.3
Multiplicity 17.7 16.8 17.7
CC(1/2) 0.999 0.999 0.350
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Files: