5RG1
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00024905
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 | 2020-03-05 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9126 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.585, 52.610, 44.852 |
Unit cell angles | 90.00, 103.09, 90.00 |
Refinement procedure
Resolution | 54.830 - 1.650 |
R-factor | 0.1741 |
Rwork | 0.172 |
R-free | 0.21520 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.541 |
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] | 54.840 | 54.840 | 1.680 |
High resolution limit [Å] | 1.650 | 9.040 | 1.650 |
Rmerge | 0.143 | 0.075 | 1.463 |
Rmeas | 0.168 | 0.086 | 1.777 |
Rpim | 0.087 | 0.042 | 0.994 |
Total number of observations | 107131 | 774 | 4358 |
Number of reflections | 30785 | ||
<I/σ(I)> | 5.1 | 15.7 | 0.9 |
Completeness [%] | 99.7 | 99.7 | 98.8 |
Redundancy | 3.5 | 3.7 | 2.9 |
CC(1/2) | 0.991 | 0.993 | 0.334 |
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 |