Table 1. Cryo-EM data collection, reconstruction, model refinement and validation statistics.
Data Collection and processing | ||||||||
---|---|---|---|---|---|---|---|---|
Microscope | Titan krios (UCSF) | |||||||
Camera | K3 detector equipped with GIF | |||||||
Magnification | 60,010 | |||||||
Voltage (kV) | 300 kV | |||||||
Electron exposure (e-/Å2) | 51 | |||||||
Defocus range (µm) | −0.5 to −2.0 | |||||||
Pixel size (Å) | 0.8332 | |||||||
Software | SerialEM | |||||||
Reconstruction | CIII2 | SCIII2+IV | CIII2 focused | CIV-focused | SC Composite | |||
Software | cryoSPARC | cryoSPARC | Relion | Relion | Phenix | |||
Number of particles | 48,111 | 28,020 | 38,410 | 29,348 | --- | |||
Box size (pixels) | 512 | 512 | 512 | 512 | 512 | |||
Final resolution (Å) | 3.2 | 3.8 | 3.7 | 3.8 | --- | |||
Map sharpening B factor (Å2) | 67 | 61 | 83 | 77 | --- | |||
EMDB ID | 22445 | 22449 | 22450 | 22447 | 22448 | |||
Model | CIII2 | CIV | SC composite | |||||
Software | Phenix | |||||||
Initial model (PDB code) | 6Q9E, 6HU9 | 6HU9, 5B1A | 6Q9E, 6HU9, 5B1A | |||||
Map/model correlation | ||||||||
Model resolution (Å) | 3.3 | 3.9 | 3.9 | |||||
d99 (Å) | 3.5 | 3.9 | 3.9 | |||||
FSC model 0.5 (Å) | 3.3 | 3.8 | 3.8 | |||||
Map CC (around atoms) | 0.88 | 0.85 | 0.84 | |||||
Model composition | ||||||||
Non-hydrogen atoms | 32,931 | 12,772 | 45,164 | |||||
Protein residues | 3983 | 1497 | 5472 | |||||
Number of chains | 20 | 10 | 30 | |||||
Number of ligands and cofactors | 8 | 6 | 14 | |||||
Number of lipids | 29 | 20 | 43 | |||||
Atomic Displacement Parameters (ADP) | ||||||||
Protein average (Å2) | 114.37 | 38.28 | 53.17 | |||||
Ligand average (Å2) | 79.11 | 50.71 | 66.25 | |||||
R.m.s. deviations | ||||||||
Bond lengths (Å) | 0.005 | 0.006 | 0.007 | |||||
Bond angles (°) | 0.704 | 0.853 | 1.107 | |||||
Ramachandran Plot | ||||||||
Favored (%) | 93.13 | 90.75 | 92.55 | |||||
Allowed (%) | 6.82 | 9.18 | 7.40 | |||||
Disallowed (%) | 0.05 | 0.07 | 0.06 | |||||
Validation | ||||||||
MolProbity score | 1.97 | 2.19 | 2.04 | |||||
Clash score | 10.03 | 14.21 | 11.51 | |||||
Rotamer outliers (%) | 0.03 | 0.08 | 0.04 | |||||
EMRinger score | 2.80 | 2.32 | 2.01 | |||||
PDB ID | 7JRG | 7JRO | 7JRP |