5RGV
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4444622066 (Mpro-x2563)
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 | 112.826, 53.189, 45.113 |
Unit cell angles | 90.00, 101.86, 90.00 |
Refinement procedure
Resolution | 55.210 - 1.820 |
R-factor | 0.1894 |
Rwork | 0.187 |
R-free | 0.23190 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.008 |
RMSD bond angle | 0.950 |
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] | 55.200 | 55.200 | 1.860 |
High resolution limit [Å] | 1.820 | 9.090 | 1.820 |
Rmerge | 0.062 | 0.026 | 2.064 |
Rmeas | 0.075 | 0.031 | 2.465 |
Rpim | 0.041 | 0.016 | 1.335 |
Total number of observations | 76876 | 698 | 4380 |
Number of reflections | 23584 | ||
<I/σ(I)> | 7.6 | 33.4 | 0.4 |
Completeness [%] | 99.7 | 99.7 | 96.7 |
Redundancy | 3.3 | 3.4 | 3.3 |
CC(1/2) | 0.999 | 0.998 | 0.324 |
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 |