15RO
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005639
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRL BEAMLINE BL12-2 |
| Synchrotron site | SSRL |
| Beamline | BL12-2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2024-03-13 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.77488 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.725, 88.725, 39.596 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.570 - 0.920 |
| R-factor | 0.1513 |
| Rwork | 0.150 |
| R-free | 0.16780 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.702 |
| Data reduction software | XDS (Jan 19, 2025 BUILT=20250430) |
| Data scaling software | Aimless (0.8.2) |
| Phasing software | PHASER (2.8.3) |
| Refinement software | PHENIX |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 44.360 | 44.360 | 0.940 |
| High resolution limit [Å] | 0.920 | 5.040 | 0.920 |
| Rmerge | 0.035 | 0.026 | 1.494 |
| Rmeas | 0.038 | 0.028 | 1.749 |
| Rpim | 0.014 | 0.011 | 0.872 |
| Total number of observations | 1377066 | 9200 | 36894 |
| Number of reflections | 212508 | 1377 | 10036 |
| <I/σ(I)> | 18.6 | 63.6 | 0.6 |
| Completeness [%] | 99.7 | 99 | 95.7 |
| Redundancy | 6.5 | 6.7 | 3.7 |
| CC(1/2) | 1.000 | 0.997 | 0.400 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
