Table 1.
Cryo‐EM data collection, refinement and validation statistics
| H2A.B‐NCP (EMD‐30078) (PDB 6M4H) | Pb‐H2A.B‐NCP C1 symmetry | Pb‐H2A.B‐NCP C2 symmetry (EMD‐30077) (PDB 6M4G) | Pb‐H2A.B‐NCP Class 2 | H2A.Z.2.2‐NCP (EMD‐30076) (PDB 6M4D) | |
|---|---|---|---|---|---|
| Data collection and processing | |||||
| Microscope | Titan Krios | Titan Krios | Titan Krios | Titan Krios | Titan Krios |
| Camera | K2 Summit | K2 Summit | K2 Summit | K2 Summit | K2 Summit |
| Magnification | 130,000 | 130,000 | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
| Pixel size (Å) | 1.04 | 1.04 | 1.04 | 1.04 | 1.04 |
| Electron exposure (e−/Å2) | 50 | 50 | 50 | 50 | 50 |
| Exposure per frame (e−/Å2) | 1.35 | 1.35 | 1.35 | 1.35 | 1.5 |
| Number of frames collected | 37 | 37 | 37 | 37 | 32 |
| Defocus range (μm) | −0.4 to −1.0 | −0.4 to −1.0 | −0.4 to −1.0 | −0.4 to −1.0 | −2.0 to −3.0 |
| Phase shift (π) | 0.2 to 0.8 | 0.2 to 0.8 | 0.2 to 0.8 | 0.2 to 0.8 | — |
| Symmetry imposed | C2 | C1 | C2 | C1 | C2 |
| Micrographs recorded/used (no.) | 1,918/1,700 | 3,130/2,086 | 3,130/2,086 | 3,130/2,086 | 1,201/1,020 |
| Initial particle images (no.) | 141,738 | 416,922 | 416,922 | 416,922 | 181,600 |
| Final particle images (no.) | 38,472 | 110,355 | 62,980 | 77,017 | 111,800 |
| Final reconstruction package | cryoSPARC | cisTEM | cisTEM | RELION‐3.0 | RELION‐3.0 |
| Map resolution (Å) | 3.9 | 3.2 | 2.8 | 6.2 | 4.4 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Refinement | |||||
| Initial model used (PDB) | 2CV5 | 2CV5 | 1F66 | ||
| Model composition | |||||
| Non‐hydrogen atoms | 9,420 | 9,032 | 10,303 | ||
| Protein residues | 656 | 657 | 682 | ||
| Ligands | 0.00 | 0.00 | 0.00 | ||
| Validation | |||||
| MolProbity score | 1.86 | 1.42 | 2.17 | ||
| Clashscore | 12.21 | 5.11 | 21.88 | ||
| Poor rotamers (%) | 0 | 0.71 | 0.00 | ||
| Ramachandran plot | |||||
| Favored (%) | 97.19 | 97.19 | 95.20 | ||
| Allowed (%) | 2.81 | 2.81 | 3.00 | ||
| Disallowed (%) | 0.00 | 0.00 | 1.80 | ||