Table 4:
Statistics for cryoEM structure of Fab 3B4 / Fab 3H4 / HAstV1 spike complex
| Data collection information | PNCC #160258 - Krios-3 |
|---|---|
|
| |
| Nominal magnification | 105,000x |
| Voltage (kV) | 300 |
| Electron dose (e-/Å2) | 32.26 |
| Physical pixel size (super-res) (Å) | 0.415 |
| Movies amount | 7,235 |
| Defocus average and range (μm) | −1.5 (−2.5 to −0.5) |
| Frames | 60 |
|
| |
| Single-particle reconstruction information | EMDB 45427 |
|
| |
| Initial particles picked | 4,132,753 |
| Particles in the final map | 163,237 |
| Initial model used | PDB 5EWO, ab-initio |
| Symmetry imposed | C1 |
| Map overall resolution - FSC0.143 (Å) | 3.33 |
| Map resolution range (Å) | 3.0–4.2 |
| Map sharpening | |
| B-factor (Å2) | −112 |
|
| |
| Built model information | PDB 9CBN |
|
| |
| Chains | 11 |
| Atoms (non-H) | 10967 |
| Protein residues | 1,040 |
| Water | 0 |
| Ligands: | |
| BMA: | 2 |
| NAG: | 5 |
|
| |
| Bonds (RMSD) | |
| Length (A, # > 4σ ) | 0.020 (2) |
| Angles (°,# > 4σ ) | 1.536 (91) |
| Mean B-factor (Å2) | |
| Protein | 0.78/102.01/40.47 |
| Nucleotide | N/A |
| Ligand | 30.00/56.36/50.22 |
| Water | N/A |
| MolProbity score | 2.72 |
| Clashscore | 31.17 |
| Ramachandran plot | |
| Favored (%) | 92.24 |
| Allowed (%) | 7.76 |
| Outliers (%) | 0 |
|
| |
| Rama-Z (Ramachandran plot Z-score, RMSD) | |
| Whole (N = 3625) | −2.05 (0.26) |
| Helix (N = 1443) | −5.16 (0.42) |
| Sheet (N = 472) | −1.26 (0.26) |
| Loop(N =1710) | −1.36 (0.25) |
|
| |
| Rotamer outliers (%) | 2.22 |
| Cβ outliers (%) | 1.77 |
|
| |
| Peptide plane (%) | |
| Cis proline/general | 7.3/0.0 |
| Twisted proline/general | 0.0/0.0 |
|
| |
| CaBLAM outliers (%) | 3.49 |
|
| |
| Occupancy | |
| Mean | 1 |
| occ = 1 (%) | 99.26 |
| 0 < occ < 1 (%) | 0.74 |
| occ > 1 (%) | 0 |
|
| |
| Model vs. Data | |
| Mean CC for ligands | 0.64 |
| CC (peaks) | 0.64 |
| CC (volume) | 0.75 |
| CC (box) | 0.7 |
| CC (mask) | 0.78 |