Table 1.
Data collection and refinement statistics.
| SARS-CoV-2 Mpro- AG7404 (PDB 7ZQV) |
SARS-CoV-1 Mpro- AG7404 (PDB 7ZQW) |
SARS-CoV-2 Mpro- Rupintrivir (PDB 7P35) |
|
|---|---|---|---|
| Data collection statistics | |||
| Space group | P21 | P21212 | P21 |
| Unit-cell dimensions (Å, °) | a = 45.31, b = 54.08, c = 115.011, α = 90.00, β = 100.34, γ = 90.00 | a = 106.854, b = 45.22, c = 53.55, α = 90.00, β = 90.00, γ = 90.00 | a = 45.02, b = 54.02, c = 114.07, α = 90.00, β = 100.77, γ = 90.00 |
| Beamline | ID30A-3 (ESRF) | XALOC (ALBA) | XALOC (ALBA) |
| Wavelength (Å) | 0.96770 | 0.97918 | 0.97926 |
| Vm (Å/Da) | 2.06 | 1.91 | 2.03 |
| Solvent content (%) | 40.00 | 35.71 | 39.44 |
| Resolution range (Å) | 48.79–2.26 (2.45–2.26) | 47.87–2.53 (2.69–2.53) | 56.09–2.26 (2.29–2.26) |
| Number of observed reflections | 47,666 (2,657) | 32,205 (1,985) | 53,621 (2,639) |
| Number of unique reflections | 18,801 (941) | 7,634 (382) | 21,599 (1,085) |
| Rmergea | 0.096 (0.552) | 0.093 (1.495) | 0.060 (0.853) |
| CC1/2 | 0.985 (0.802) | 0.998 (0.431) | 0.998 (0.580) |
| Spherical completeness (%) | 72.7 (17.5) | 83.1 (24.5) | 84.4 (87.9) |
| Ellipsoidal completeness (%)b | 89.5 (56.8) | 91.9 (46.3) | |
| Mean I/σ (I) | 4.5 (1.4) | 10.1 (1.1) | 9.6 (1.4) |
| Multiplicity | 2.5 (2.8) | 4.2 (5.2) | 2.5 (2.4) |
| Refinement statistics | |||
| Rfactorc | 0.190 | 0.215 | 0.200 |
| Rfreec | 0.241 | 0.289 | 0.258 |
| Number of atoms (non-H) | 4,896 | 2,375 | 4,814 |
|
4,716 | 2,336 | 4,694 |
|
76 | 38 | 86 |
|
104 | 1 | 34 |
| r.m.s.d. for bond lengths (Å) | 0.006 | 0.006 | 0.006 |
| r.m.s.d. for bond angles (°) | 1.444 | 1.526 | 1.471 |
| Average B-factor (Å2) | 40.67 | 65.93 | 50.93 |
| Average B-factor for inhibitor molecules (Å2) | 60.92 (62.68 for chain A, 59.15 for chain B) | 82.69 | 94.59 (98.95 for chain A, 90.22 for chain B) |
| Ramachandran analysisd | |||
| Residues in allowed regions (%) | 99.67 | 99.67 | 99.34 |
| Residues in outlier regions (%) | 0.33 | 0.33 | 0.66 |
Values in parenthesis refer to the outer-most resolution shell.
a
Rmerge = ΣℎΣi∣Ii,ℎ−<Iℎ>∣/ΣℎΣiIi, where Ii,h is the ith-intensity measurement of reflection h and <Ih> is the average intensity for multiple measurements.
b
Ellipsoidal completeness was calculated with STARANISO (Tickle et al., 2018).
c
Rfactor and Rfree = Σ||Fo|−|Fc||/Σ|Fo|. Rfree was calculated for 5% of the reflections not used for refinement.
d
Ramachandran analysis was done with MolProbity (Chen et al., 2010).