15IX
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005066
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) | 0.88555 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.703, 88.703, 39.429 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 44.350 - 1.000 |
| R-factor | 0.1573 |
| Rwork | 0.157 |
| R-free | 0.17340 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.707 |
| 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] | 44.350 | 44.350 | 1.020 |
| High resolution limit [Å] | 1.000 | 5.480 | 1.000 |
| Rmerge | 0.047 | 0.033 | 1.407 |
| Rmeas | 0.052 | 0.036 | 1.576 |
| Rpim | 0.020 | 0.014 | 0.693 |
| Total number of observations | 1050272 | 7497 | 36624 |
| Number of reflections | 164960 | 1093 | 7592 |
| <I/σ(I)> | 13.8 | 50.5 | 0.8 |
| Completeness [%] | 99.6 | 99.9 | 93.1 |
| Redundancy | 6.4 | 6.9 | 4.8 |
| CC(1/2) | 0.999 | 0.998 | 0.678 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
