5RGP
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102628 (Mpro-x0771)
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 | 2020-03-04 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9126 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.840, 53.000, 44.340 |
Unit cell angles | 90.00, 103.00, 90.00 |
Refinement procedure
Resolution | 54.970 - 2.070 |
R-factor | 0.163 |
Rwork | 0.161 |
R-free | 0.20190 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6lu7 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.511 |
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] | 54.970 | 54.970 | 2.120 |
High resolution limit [Å] | 2.070 | 9.260 | 2.070 |
Rmerge | 0.130 | 0.037 | 0.766 |
Rmeas | 0.156 | 0.045 | 0.927 |
Rpim | 0.085 | 0.025 | 0.515 |
Total number of observations | 50900 | 631 | 3351 |
Number of reflections | 15618 | ||
<I/σ(I)> | 6.6 | 22.9 | 1.4 |
Completeness [%] | 99.5 | 98.8 | 95.7 |
Redundancy | 3.3 | 3.3 | 3 |
CC(1/2) | 0.991 | 0.996 | 0.585 |
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 |