5SMN
PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z1365651030 (Mpro-IBM0078)
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 | 2020-11-26 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.91263 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 111.926, 52.568, 44.593 |
| Unit cell angles | 90.00, 102.93, 90.00 |
Refinement procedure
| Resolution | 54.540 - 1.360 |
| R-factor | 0.1885 |
| Rwork | 0.187 |
| R-free | 0.21160 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 6lu7 |
| RMSD bond length | 0.011 |
| RMSD bond angle | 1.630 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.7.7) |
| Phasing software | REFMAC |
| Refinement software | REFMAC (5.8.0267) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 54.520 | 54.520 | 1.380 |
| High resolution limit [Å] | 1.360 | 7.440 | 1.360 |
| Rmerge | 0.068 | 0.020 | 1.069 |
| Rmeas | 0.082 | 0.023 | 1.395 |
| Rpim | 0.046 | 0.013 | 0.885 |
| Total number of observations | 158683 | 1218 | 5261 |
| Number of reflections | 53628 | ||
| <I/σ(I)> | 14.6 | 103.5 | 0.7 |
| Completeness [%] | 98.8 | 99.8 | 91.8 |
| Redundancy | 3 | 3.4 | 2.1 |
| CC(1/2) | 0.998 | 0.999 | 0.304 |
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 |
