5RGG
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434890 (Mpro-x0165)
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 | 2020-02-26 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9126 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.030, 52.760, 44.570 |
Unit cell angles | 90.00, 102.50, 90.00 |
Refinement procedure
Resolution | 47.520 - 2.260 |
R-factor | 0.1689 |
Rwork | 0.167 |
R-free | 0.21650 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.006 |
RMSD bond angle | 1.435 |
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] | 54.610 | 54.610 | 2.330 |
High resolution limit [Å] | 2.250 | 9.010 | 2.250 |
Rmerge | 0.338 | 0.057 | 2.445 |
Rmeas | 0.407 | 0.066 | 3.016 |
Rpim | 0.221 | 0.032 | 1.727 |
Total number of observations | 40647 | 783 | 3573 |
Number of reflections | 12065 | ||
<I/σ(I)> | 4.4 | 10.7 | 1.6 |
Completeness [%] | 99.4 | 99.7 | 97.1 |
Redundancy | 3.4 | 3.8 | 3.3 |
CC(1/2) | 0.823 | 0.995 | 0.061 |
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 |