5RG2
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00025058
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-03-05 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9126 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.605, 52.589, 44.578 |
Unit cell angles | 90.00, 102.94, 90.00 |
Refinement procedure
Resolution | 54.870 - 1.630 |
R-factor | 0.1853 |
Rwork | 0.183 |
R-free | 0.22830 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.522 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 54.900 | 54.900 | 1.660 |
High resolution limit [Å] | 1.630 | 8.930 | 1.630 |
Rmerge | 0.127 | 0.035 | 1.461 |
Rmeas | 0.150 | 0.041 | 1.800 |
Rpim | 0.078 | 0.021 | 1.033 |
Total number of observations | 110832 | 808 | 4310 |
Number of reflections | 31775 | ||
<I/σ(I)> | 5.9 | 23.5 | 0.7 |
Completeness [%] | 99.7 | 99.7 | 97.4 |
Redundancy | 3.5 | 3.8 | 2.8 |
CC(1/2) | 0.995 | 0.997 | 0.311 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293.15 | 15% PEG 4K, 5% DMSO, 0.1M MES pH 6.5 |