5RGI
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z369936976 (Mpro-x0397)
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 | 2020-02-27 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9126 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.159, 52.655, 44.500 |
Unit cell angles | 90.00, 102.97, 90.00 |
Refinement procedure
Resolution | 54.650 - 1.570 |
R-factor | 0.1724 |
Rwork | 0.170 |
R-free | 0.21170 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.566 |
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] | 54.650 | 54.650 | 1.600 |
High resolution limit [Å] | 1.570 | 8.600 | 1.570 |
Rmerge | 0.096 | 0.028 | 1.186 |
Rmeas | 0.114 | 0.033 | 1.461 |
Rpim | 0.060 | 0.017 | 0.842 |
Total number of observations | 117587 | 892 | 4341 |
Number of reflections | 35209 | ||
<I/σ(I)> | 7.2 | 28.2 | 0.9 |
Completeness [%] | 99.4 | 99.8 | 95.1 |
Redundancy | 3.3 | 3.8 | 2.6 |
CC(1/2) | 0.997 | 0.999 | 0.380 |
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 |