9AZX
Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with NDPr
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | CHESS BEAMLINE 7B2 |
Synchrotron site | CHESS |
Beamline | 7B2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-01-26 |
Detector | DECTRIS EIGER2 S 16M |
Wavelength(s) | 0.96860 |
Spacegroup name | P 1 |
Unit cell lengths | 45.496, 47.084, 65.726 |
Unit cell angles | 79.15, 72.05, 74.30 |
Refinement procedure
Resolution | 29.060 - 1.395 |
R-factor | 0.153 |
Rwork | 0.152 |
R-free | 0.18440 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6ywl |
RMSD bond length | 0.010 |
RMSD bond angle | 1.093 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.21_5207) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 29.060 | 1.430 |
High resolution limit [Å] | 1.395 | 1.395 |
Rmerge | 0.054 | 0.601 |
Rmeas | 0.064 | 0.747 |
Rpim | 0.034 | 0.434 |
Number of reflections | 93149 | 5586 |
<I/σ(I)> | 12.18 | 1.38 |
Completeness [%] | 94.3 | 78.78 |
Redundancy | 3.5 | 2.7 |
CC(1/2) | 0.998 | 0.728 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 100 mM Tris-HCl, pH 8, 200 mM sodium acetate, 30% w/v PEG4000 |