15II
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004999
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 | 2023-12-19 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 0.88557 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.715, 88.715, 39.410 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 44.360 - 1.000 |
| R-factor | 0.1619 |
| Rwork | 0.161 |
| R-free | 0.18160 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.723 |
| 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 | 1.020 |
| High resolution limit [Å] | 1.000 | 5.480 | 1.000 |
| Rmerge | 0.041 | 0.026 | 1.944 |
| Rmeas | 0.045 | 0.029 | 2.188 |
| Rpim | 0.018 | 0.011 | 0.985 |
| Total number of observations | 1057427 | 7463 | 36852 |
| Number of reflections | 165233 | 1090 | 7889 |
| <I/σ(I)> | 16.1 | 75 | 0.7 |
| Completeness [%] | 99.8 | 99.8 | 96.6 |
| Redundancy | 6.4 | 6.8 | 4.7 |
| CC(1/2) | 1.000 | 0.999 | 0.475 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
