15PI
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005526
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 | 2024-02-14 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.77488 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.776, 88.776, 39.626 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 39.700 - 0.960 |
| R-factor | 0.1504 |
| Rwork | 0.150 |
| R-free | 0.16370 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.731 |
| 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] | 44.390 | 44.390 | 0.980 |
| High resolution limit [Å] | 0.960 | 5.260 | 0.960 |
| Rmerge | 0.046 | 0.028 | 2.475 |
| Rmeas | 0.050 | 0.030 | 2.695 |
| Rpim | 0.019 | 0.011 | 1.051 |
| Total number of observations | 1268071 | 8376 | 57956 |
| Number of reflections | 187378 | 1227 | 9003 |
| <I/σ(I)> | 15.1 | 51.3 | 0.6 |
| Completeness [%] | 99.6 | 99.4 | 96.8 |
| Redundancy | 6.8 | 6.8 | 6.4 |
| CC(1/2) | 0.999 | 0.999 | 0.384 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
