Table 1 Cryo-EM data collection and refinement statistics.
3dSpike-Fab6 (PDB 7MW2) (EMD-24060) | 2dSpike-Fab6 (PDB 7MW3) (EMD-24061) | 1dSpike-Fab6 (PDB 7MW4) (EMD-24062) | 2uSpike-Fab2 (PDB 7MW5) (EMD-24063) | 3uSpike-Fab2 (PDB 7MW6) (EMD-24064) | |
|---|---|---|---|---|---|
Data collection and processing | |||||
Magnification | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 66.5 | 66.5 | 66.5 | 66.5 | 66.5 |
Defocus range (μm) | −0.8 to −1.8 | −0.8 to −1.8 | −0.8 to −1.8 | −0.8 to −1.8 | −0.8 to −1.8 |
Pixel size (Å) | 1.068 | 1.068 | 1.068 | 1.068 | 1.068 |
Symmetry imposed | C3 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 655318 | 1013040 | |||
Final particle images (no.) | 68416 | 111449 | 80954 | 135336 | 181380 |
Map resolution (Å) FSC threshold | 2.97 | 3.15 | 3.42 | 3.42 | 3.22 |
Refinement | |||||
Map sharpening B factor (Å2) | −81 to −91 | −69 to −127 | −76 to −142 | −74 to −189 | −80 to −100 |
Model map FSC (masked) | 0.83 | 0.81 | 0.74 | 0.67 | 0.69 |
Model composition | |||||
Non-hydrogen atoms | 33,807 | 33,825 | 33,741 | 33,661 | 35,247 |
Protein residues | 4293 | 4293 | 4290 | 4245 | 4446 |
Ligands | 72 | 72 | 74 | 83 | 87 |
B factors (Å2) | |||||
Protein | 41 | 46 | 63 | 118 | 39 |
Ligand | 80 | 69 | 94 | 156 | 62 |
R.m.s. deviations | |||||
Bond lengths (Å) | 0.003 | 0.003 | 0.003 | 0.003 | 0.004 |
Bond angles (°) | 0.6 | 0.6 | 0.6 | 0.7 | 0.8 |
Validation | |||||
MolProbity score | 1.6 | 1.7 | 1.8 | 2.2 | 2.0 |
Clashscore | 7.1 | 7.5 | 8.7 | 14.1 | 11.0 |
Poor rotamers (%) | 0.08 | 0.08 | 0.11 | 0.08 | 0.11 |
Ramachandran plot | |||||
Favored (%) | 96.68 | 96.09 | 95.64 | 91.39 | 94.27 |
Allowed (%) | 3.15 | 3.55 | 4.15 | 8.03 | 5.06 |
Disallowed (%) | 0.17 | 0.36 | 0.21 | 0.57 | 0.66 |
