15RF
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005123
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 | 88.736, 88.736, 39.485 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 39.680 - 0.970 |
| R-factor | 0.1406 |
| Rwork | 0.140 |
| R-free | 0.15730 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.737 |
| 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] | 44.370 | 44.370 | 0.990 |
| High resolution limit [Å] | 0.970 | 5.310 | 0.970 |
| Rmerge | 0.041 | 0.026 | 1.546 |
| Rmeas | 0.045 | 0.028 | 1.678 |
| Rpim | 0.017 | 0.011 | 0.644 |
| Total number of observations | 1223675 | 8032 | 58788 |
| Number of reflections | 180508 | 1182 | 8894 |
| <I/σ(I)> | 16.3 | 56.4 | 1 |
| Completeness [%] | 99.4 | 99.1 | 98.8 |
| Redundancy | 6.8 | 6.8 | 6.6 |
| CC(1/2) | 1.000 | 0.999 | 0.725 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
