15PC
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005700
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 | 2023-12-22 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 0.88557 |
| Spacegroup name | P 43 |
| Unit cell lengths | 88.766, 88.766, 39.494 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 44.380 - 1.000 |
| R-factor | 0.1412 |
| Rwork | 0.140 |
| R-free | 0.15780 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.724 |
| 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 | 1.020 |
| High resolution limit [Å] | 1.000 | 5.480 | 1.000 |
| Rmerge | 0.063 | 0.031 | 1.096 |
| Rmeas | 0.069 | 0.033 | 1.229 |
| Rpim | 0.027 | 0.013 | 0.543 |
| Total number of observations | 1045048 | 7455 | 36178 |
| Number of reflections | 165393 | 1095 | 7575 |
| <I/σ(I)> | 11.2 | 34 | 0.8 |
| Completeness [%] | 99.6 | 99.9 | 92.6 |
| Redundancy | 6.3 | 6.8 | 4.8 |
| CC(1/2) | 0.999 | 0.998 | 0.663 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 292 | 100 mM CHES, 28% PEG 3000 |
