8VDJ
Crystal structure of SARS-CoV-2 3CL protease (3CLpro) as a covalent complex with EDP-235
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 17-ID |
Synchrotron site | APS |
Beamline | 17-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-07-10 |
Detector | DECTRIS EIGER2 X 9M |
Wavelength(s) | 1.000 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 67.451, 99.130, 100.626 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 31.770 - 2.002 |
R-factor | 0.2369 |
Rwork | 0.235 |
R-free | 0.27070 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.008 |
RMSD bond angle | 0.650 |
Data reduction software | XDS (Feb 5, 2021 (BUILT 20210323)) |
Data scaling software | Aimless (0.7.7) |
Phasing software | PHASER |
Refinement software | BUSTER (2.11.8 (8-JUN-2022)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 70.618 | 70.618 | 2.219 |
High resolution limit [Å] | 2.002 | 6.863 | 2.002 |
Rmerge | 0.126 | 0.044 | 0.833 |
Rmeas | 0.137 | 0.048 | 0.908 |
Rpim | 0.054 | 0.019 | 0.359 |
Total number of observations | 165074 | 8175 | 7910 |
Number of reflections | 25441 | 1272 | 1272 |
<I/σ(I)> | 9.73 | 25.39 | 2.17 |
Completeness [%] | 85.8 | 99.4 | 63.3 |
Completeness (spherical) [%] | 55.1 | 99.4 | 10.6 |
Completeness (ellipsoidal) [%] | 85.8 | 99.4 | 63.3 |
Redundancy | 6.49 | 6.43 | 6.22 |
CC(1/2) | 0.998 | 0.999 | 0.595 |
Anomalous completeness (spherical) | 53.8 | 99.8 | 10.1 |
Anomalous completeness | 85.0 | 99.8 | 62.9 |
Anomalous redundancy | 3.5 | 3.8 | 3.3 |
CC(ano) | -0.203 | -0.426 | 0.001 |
|DANO|/σ(DANO) | 0.7 | 0.5 | 0.8 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
1.920 Å | 1.000, 1.000, 1.000 |
2.832 Å | 0.000, 0.000, 0.000 |
2.309 Å | 0.000, 0.000, 0.000 |
Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | The protein solution was incubated with DTT (0.22 mM) for 10 min on ice. Compound EDP-235 in DMSO (2.88 mM) was then added and incubated for 3 hrs on ice, then for 20 min at 18 C. Crystals appeared in drop with reservoir conditions: 0.2 M sodium thiocyanate, 20 % w/v PEG3350. The sample was harvested after 10 days growth and transferred to drop of neat reservoir condition. Cryoprotection was achieved by supplementing this drop with additional PEG400 to a final concentration of 5 % w/v PEG400 in reservoir condition. The sample was cryocooled by plunging into liquid nitrogen. |