Table 3 Cryo-EM data collection, processing, and structure refinement
Data sets | Free falcilysin | Falcilysin + MK-4815 | ||
|---|---|---|---|---|
Conformations | Open | Partially closed | Open | Partially closed |
(EMD-37941) | (EMD-37940) | (EMD-37939) | (EMD-37938) | |
(PDB 8WYY) | (PDB 8WYX) | (PDB 8WYU) | (PDB 8WYT) | |
Data collection and processing | ||||
Magnification | 215,000 | 215,000 | ||
Voltage (kV) | 300 | 300 | ||
Electron exposure (e–/Å2) | 40 | 40 | ||
Defocus range (μm) | −2.5 to −0.5 | −2.5 to −0.5 | ||
Pixel size (Å) | 0.573 | 0.58 | ||
Symmetry imposed | C1 | C1 | ||
Initial particle images (no.) | 385,133 | 171,640 | 88,926 | 168,840 |
Final particle images (no.) | 101,660 | 50,355 | 45,566 | 98,298 |
Map resolution (Å) | 3.1 | 3.5 | 3.2 | 2.7 |
FSC threshold = 0.143 | ||||
3D-FSC sphericity | 0.863 | 0.778 | 0.770 | 0.864 |
Refinement | ||||
Initial model used (PDB code) | 3S5M | 3S5M | 3S5M | 3S5M |
Model resolution (Å) | 3.12 | 4.17 | 3.43 | 2.77 |
FSC threshold = 0.5 | ||||
Map sharpening B factor (Å2) | −79.48 | −101.68 | −75.98 | −66.33 |
Model composition | ||||
Non-hydrogen atoms | 8795 | 8809 | 8819 | 8826 |
Protein residues | 1069 | 1070 | 1072 | 1070 |
MK-4815 | 0 | 0 | 0 | 1 |
Zinc | 1 | 1 | 1 | 1 |
B factors (Å2) | ||||
Protein | 109.09 | 156.03 | 116.19 | 83.47 |
MK-4815 | N.A. | N.A. | N.A. | 68.72 |
Zinc | 162.00 | 175.20 | 158.98 | 137.20 |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.007 | 0.005 | 0.006 | 0.006 |
Bond angles (°) | 0.746 | 0.569 | 0.808 | 0.574 |
Validation | ||||
MolProbity score | 1.90 | 1.72 | 2.07 | 1.70 |
Clashscore | 12.64 | 10.00 | 18.85 | 9.82 |
Poor rotamers (%) | 0.20 | 0.20 | 0.51 | 0.20 |
Ramachandran plot | ||||
Favored (%) | 95.85 | 96.80 | 95.77 | 96.89 |
Allowed (%) | 4.05 | 3.20 | 4.23 | 3.11 |
Disallowed (%) | 0.09 | 0.00 | 0.00 | 0.00 |
