5RGW
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4444621910 (Mpro-x2569)
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 | 2020-04-21 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.913 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.384, 52.739, 44.458 |
Unit cell angles | 90.00, 102.79, 90.00 |
Refinement procedure
Resolution | 54.800 - 1.430 |
R-factor | 0.181 |
Rwork | 0.180 |
R-free | 0.20330 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.008 |
RMSD bond angle | 0.980 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | REFMAC |
Refinement software | BUSTER (2.10.3 (29-NOV-2019)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 54.840 | 54.840 | 1.450 |
High resolution limit [Å] | 1.430 | 7.830 | 1.430 |
Rmerge | 0.045 | 0.020 | 1.129 |
Rmeas | 0.054 | 0.023 | 1.505 |
Rpim | 0.031 | 0.013 | 0.985 |
Total number of observations | 125208 | 1005 | 3814 |
Number of reflections | 45973 | ||
<I/σ(I)> | 8.4 | 35.1 | 0.5 |
Completeness [%] | 98.0 | 99.8 | 93.9 |
Redundancy | 2.7 | 3.2 | 1.8 |
CC(1/2) | 0.999 | 0.999 | 0.282 |
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 |