5RL3
PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors -- Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-39 (Mpro-x3117)
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 | 2020-05-14 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9126 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 113.059, 52.832, 44.547 |
Unit cell angles | 90.00, 103.02, 90.00 |
Refinement procedure
Resolution | 55.080 - 1.510 |
R-factor | 0.1785 |
Rwork | 0.177 |
R-free | 0.20490 |
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 (20-MAY-2020)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 55.120 | 55.120 | 1.540 |
High resolution limit [Å] | 1.510 | 8.270 | 1.510 |
Rmerge | 0.075 | 0.026 | 1.088 |
Rmeas | 0.089 | 0.030 | 1.386 |
Rpim | 0.047 | 0.016 | 0.845 |
Total number of observations | 128178 | 1006 | 4258 |
Number of reflections | 39869 | ||
<I/σ(I)> | 7.4 | 28.9 | 0.7 |
Completeness [%] | 99.0 | 99.8 | 95.4 |
Redundancy | 3.2 | 3.7 | 2.2 |
CC(1/2) | 0.997 | 0.998 | 0.359 |
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 |