15DM
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006022
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SSRL BEAMLINE BL9-2 |
| Synchrotron site | SSRL |
| Beamline | BL9-2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-08-11 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.88557 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.723, 88.723, 39.522 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 39.680 - 1.010 |
| R-factor | 0.1484 |
| Rwork | 0.148 |
| R-free | 0.16350 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.713 |
| 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 | 1.030 |
| High resolution limit [Å] | 1.010 | 5.530 | 1.010 |
| Rmerge | 0.047 | 0.030 | 1.667 |
| Rmeas | 0.051 | 0.033 | 1.818 |
| Rpim | 0.020 | 0.012 | 0.714 |
| Total number of observations | 1049004 | 7490 | 48545 |
| Number of reflections | 159709 | 1066 | 7779 |
| <I/σ(I)> | 15.9 | 65.6 | 1.1 |
| Completeness [%] | 99.2 | 99.7 | 98.2 |
| Redundancy | 6.6 | 7 | 6.2 |
| CC(1/2) | 0.999 | 0.999 | 0.715 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
