Table 1.
Cryo-EM data collection, refinement and validation statistics
| RSCSAR apo (EMD-21489, PDB 6VZG) |
RSCSAR nucleosome (BeF3) (EMD-21484, PDB 6VZ4) |
RSCSAR nucleosome (BeF3) Peeled conformation (EMD-21493) |
|
|---|---|---|---|
| Data collection and processing | |||
| Magnification | 36,000 | 36,000 | 36,000 |
| Voltage (kV) | 200 | 200 | 200 |
| Camera mode | Super-resolution | Counting | Counting |
| Electron exposure (e–/Å2) | 50–55 | 50–55 | 50–55 |
| Defocus range (μm) | 0.6–2.5 | 0.6–2.5 | 0.6–2.5 |
| Pixel size (Å) | 0.58 | 1.16 | 1.16 |
| Symmetry imposed | C1 | C1 | C1 |
| Initial particle images (no.) | 1,986,341 | 2,020,734 | 2,020,734 |
| Final particle images (no.) | 415,957 | 293,940 | 112,364 |
| Map resolution (Å) | 4.2 | 3.9 | 4.3 |
| FSC threshold | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 4.0–5.8 | 3.5–15 | |
| Refinement | |||
| Initial model used | PDB 4I6M, 5TGC | PDB 5Z3U, 5HZR | |
| Model resolution (Å) | 4.2 | 3.9 | |
| FSC threshold | 0.143 | 0.143 | |
| Model resolution range (Å) | 4.0–5.8 | 3.5–15 | |
| Map sharpening B factor (Å2) | −162 | −118 | −114 |
| Model composition | |||
| Number of models | 10 | 10 | |
| Non-hydrogen atoms (per model) | 7420 | 23950 | |
| Protein residues (per model) | 906 | 2509 | |
| Ligands (per model) | 1 ATP | 1 ADP; 1 Mg2+; 1 BeF3, 1 ATP |
|
| B factors (Å2) | |||
| Protein | 101.4 | 116.64 | |
| R.m.s. deviations | |||
| Bond lengths (Å) | 0.014 | 0.013 | |
| Bond angles (°) | 1.35 | 1.13 | |
| Validation | |||
| MolProbity score | 1.23 | 1.27 | |
| Clashscore | 1.89 | 2.08 | |
| EM Ringer Score | 1.37 | 1.77 | |
| Map CC (CC mask) | 0.791 | 0.832 | |
| Poor rotamers (%) | 0.01 | 0.26 | |
| Ramachandran plot | |||
| Favored (%) | 95.91 | 95.85 | |
| Allowed (%) | 3.18 | 3.21 | |
| Disallowed (%) | 0.91 | 0.94 |