Table 1 Crystallographic data collection and refinement statistics of Mpro and the complexes with ebselen and MR6-31-2.
From: Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives
Mpro | Mpro-ebselen | Mpro-MR6-31-2 | |
|---|---|---|---|
Data collection | |||
Space group | C2 | C2 | C2 |
Cell dimensions | |||
a, b, c (Å) | 115.35, 53.61, 44.98 | 113.20, 53.78, 44.92 | 114.00, 53.62, 44.54 |
α, β, γ (°) | 90.00, 101.37, 90.00 | 90.00, 101.44, 90.00 | 90.00, 100.89, 90.00 |
Resolution (Å) | 48.49–1.65 (1.68–1.65) | 48.39–2.05 (2.11–2.05) | 33.87–1.85 (1.89–1.85) |
Rmerge(%) | 3.7 (29.5) | 3.8 (58.5) | 7.5 (107.9) |
Rpim(%) | 3.5 (26.7) | 3.6 (53.3) | 6.9 (97.1) |
CC1/2 | 0.999 (0.899) | 0.998 (0.699) | 0.997 (0.446) |
I /σI | 13.2 (2.2) | 12.4 (1.8) | 8.6 (1.6) |
Completeness (%) | 99.9 (99.9) | 99.5 (100.0) | 99.9 (99.9) |
Redundancy | 3.3 (3.4) | 3.4 (3.5) | 3.3 (3.2) |
Refinement | |||
Resolution (Å) | 48.49–1.65 | 48.39–2.05 | 33.87–1.85 |
No. reflections | 32,461 | 16,661 | 21,465 |
Rwork /Rfree(%) | 17.60/18.70 | 20.10/22.05 | 22.39/24.90 |
No. atoms | |||
Protein | 2360 | 2324 | 2335 |
Sea | 0 | 1 | 1 |
Water | 250 | 88 | 139 |
B-factors (Å2) | |||
Protein | 15.58 | 50.12 | 36.18 |
Se | – | 52.68 | 38.72 |
Water | 37.88 | 51.39 | 39.47 |
R.m.s. deviations | |||
Bond lengths (Å) | 0.0104 | 0.0066 | 0.0068 |
Bond angles (°) | 1.712 | 1.489 | 1.572 |
Ramachandran plot | |||
Preferred (%) | 97.37 | 97.35 | 96.69 |
Allowed (%) | 2.30 | 2.32 | 3.31 |
Outliers (%) | 0.33 | 0.33 | 0 |
PDB code | 7BAJ | 7BAK | 7BAL |
