15RT
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005786
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 | 2024-03-13 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.77488 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.764, 88.764, 39.504 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.590 - 0.990 |
| R-factor | 0.1537 |
| Rwork | 0.153 |
| R-free | 0.17180 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.720 |
| 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] | 44.380 | 44.380 | 1.010 |
| High resolution limit [Å] | 0.990 | 5.420 | 0.990 |
| Rmerge | 0.041 | 0.022 | 2.754 |
| Rmeas | 0.044 | 0.024 | 2.988 |
| Rpim | 0.017 | 0.009 | 1.149 |
| Total number of observations | 1154179 | 7549 | 55794 |
| Number of reflections | 170954 | 1133 | 8373 |
| <I/σ(I)> | 16.3 | 66.5 | 0.6 |
| Completeness [%] | 99.9 | 99.8 | 99.3 |
| Redundancy | 6.8 | 6.7 | 6.7 |
| CC(1/2) | 1.000 | 1.000 | 0.347 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
