5RGH
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1619978933 (Mpro-x0395)
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 | 113.045, 52.891, 44.402 |
Unit cell angles | 90.00, 102.99, 90.00 |
Refinement procedure
Resolution | 55.080 - 1.700 |
R-factor | 0.1675 |
Rwork | 0.165 |
R-free | 0.20760 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.605 |
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] | 55.070 | 55.070 | 1.730 |
High resolution limit [Å] | 1.700 | 8.990 | 1.700 |
Rmerge | 0.111 | 0.029 | 0.978 |
Rmeas | 0.131 | 0.034 | 1.197 |
Rpim | 0.069 | 0.017 | 0.678 |
Total number of observations | 99217 | 801 | 4454 |
Number of reflections | 28162 | ||
<I/σ(I)> | 8.4 | 23.9 | 1.5 |
Completeness [%] | 99.6 | 99.7 | 97 |
Redundancy | 3.5 | 3.8 | 3 |
CC(1/2) | 0.993 | 0.998 | 0.425 |
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 |