7A1U
Structure of SARS-CoV-2 Main Protease bound to Fusidic Acid.
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 | 2020-05-20 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.0332 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 113.573, 53.489, 44.551 |
Unit cell angles | 90.00, 102.78, 90.00 |
Refinement procedure
Resolution | 55.380 - 1.670 |
R-factor | 0.1743 |
Rwork | 0.173 |
R-free | 0.20420 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6yb7 |
RMSD bond length | 0.007 |
RMSD bond angle | 0.896 |
Data reduction software | DIALS |
Data scaling software | DIALS |
Phasing software | DIMPLE |
Refinement software | REFMAC (5.8.0222) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 55.380 | 1.700 |
High resolution limit [Å] | 1.670 | 1.670 |
Rmerge | 0.075 | 0.623 |
Rmeas | 0.088 | 0.738 |
Rpim | 0.045 | 0.391 |
Number of reflections | 30352 | 1503 |
<I/σ(I)> | 8.5 | |
Completeness [%] | 99.9 | 98.49 |
Redundancy | 3.6 | 3.3 |
CC(1/2) | 0.998 | 0.506 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | Co-crystallization with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v 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 achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days. Crystals were manually harvested and flash cooled in liquid nitrogen for subsequent X-ray diffraction data collection. |