15FD
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004684
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | ALS BEAMLINE 8.3.1 |
| Synchrotron site | ALS |
| Beamline | 8.3.1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-11-18 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 0.88557 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.746, 88.746, 39.478 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 44.370 - 0.980 |
| R-factor | 0.1503 |
| Rwork | 0.149 |
| R-free | 0.16630 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.716 |
| 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 | 1.000 |
| High resolution limit [Å] | 0.980 | 5.370 | 0.980 |
| Rmerge | 0.067 | 0.052 | 1.538 |
| Rmeas | 0.073 | 0.056 | 1.806 |
| Rpim | 0.029 | 0.021 | 0.917 |
| Total number of observations | 1085787 | 7803 | 29532 |
| Number of reflections | 175724 | 1165 | 8281 |
| <I/σ(I)> | 10.1 | 32.8 | 0.5 |
| Completeness [%] | 99.7 | 99.9 | 95.5 |
| Redundancy | 6.2 | 6.7 | 3.6 |
| CC(1/2) | 0.998 | 0.997 | 0.375 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
