5RGO
PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102248 (Mpro-x0736)
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 | 2020-03-03 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9126 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 112.692, 52.831, 44.621 |
| Unit cell angles | 90.00, 103.02, 90.00 |
Refinement procedure
| Resolution | 54.900 - 1.740 |
| R-factor | 0.177 |
| Rwork | 0.175 |
| R-free | 0.21750 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 6lu7 |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.508 |
| 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] | 54.880 | 54.880 | 1.770 |
| High resolution limit [Å] | 1.740 | 9.030 | 1.740 |
| Rmerge | 0.155 | 0.034 | 1.337 |
| Rmeas | 0.182 | 0.039 | 1.622 |
| Rpim | 0.094 | 0.020 | 0.904 |
| Total number of observations | 93629 | 807 | 4306 |
| Number of reflections | 26305 | ||
| <I/σ(I)> | 5.3 | 21.3 | 0.8 |
| Completeness [%] | 99.6 | 99.7 | 97.1 |
| Redundancy | 3.6 | 3.9 | 3.1 |
| CC(1/2) | 0.992 | 0.998 | 0.326 |
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 |
