5S2Z
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z126932614
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-05-20 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.91188 |
Spacegroup name | P 43 |
Unit cell lengths | 88.180, 88.180, 38.830 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 62.350 - 1.070 |
R-factor | 0.1698 |
Rwork | 0.168 |
R-free | 0.20050 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6woj |
RMSD bond length | 0.010 |
RMSD bond angle | 1.080 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | REFMAC |
Refinement software | BUSTER (2.10.3 (20-MAY-2020)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 62.340 | 62.340 | 1.090 |
High resolution limit [Å] | 1.070 | 5.860 | 1.070 |
Rmerge | 0.084 | 0.056 | 1.480 |
Rmeas | 0.092 | 0.061 | 1.798 |
Rpim | 0.037 | 0.024 | 1.003 |
Total number of observations | 714386 | 6064 | 18748 |
Number of reflections | 131533 | ||
<I/σ(I)> | 7.2 | 24.2 | 0.6 |
Completeness [%] | 99.9 | 99.9 | 97.9 |
Redundancy | 5.4 | 6.9 | 2.9 |
CC(1/2) | 0.998 | 0.993 | 0.385 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 0.1 | 293.15 | 30% PEG 3K |