7AF0
Structure of SARS-CoV-2 Main Protease bound to Ipidacrine.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, DESY BEAMLINE P11 |
Synchrotron site | PETRA III, DESY |
Beamline | P11 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-04-29 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.0332 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 112.753, 52.960, 44.842 |
Unit cell angles | 90.00, 102.90, 90.00 |
Refinement procedure
Resolution | 27.490 - 1.700 |
R-factor | 0.1792 |
Rwork | 0.178 |
R-free | 0.22500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yb7 |
RMSD bond length | 0.011 |
RMSD bond angle | 1.428 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0222) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 27.490 | 1.761 |
High resolution limit [Å] | 1.700 | 1.700 |
Number of reflections | 28452 | 2822 |
<I/σ(I)> | 6.05 | |
Completeness [%] | 99.7 | 99.51 |
Redundancy | 3.5 | |
CC(1/2) | 0.993 | 0.764 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | COUNTER-DIFFUSION | 291 | Co-crystallization with the compounds was achieved by equilibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1 mMEDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB, pH 7.5, containing 25% w/w PEG 1500 and 5% v/v DMSO. Prior to crystallization compound solutions in DMSO were dried onto the wells of SwissCI 96-well plates. To obtain well-diffracting crystals in a reproducible way seeding was applied for crystal growth. Crystals appeared within a few hours and reached their final size after 2 - 3 days. Crystals were manually harvested and flash-frozen in liquid nitrogen for subsequent X-ray diffraction data collection. |