Table 1.
Cryo-EM data collection, refinement and validation statistics for the 4×177 and 4×187 arrays
| 4×177 | 4×187 | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nuc 1 | nuc 2 | nuc 3 | nuc 4 | stack | trinuc | tetranuc | nuc 1 | nuc 2 | nuc 3 | nuc 4 | stack | trinuc | |
| EMD-13359 | EMD-13360 | EMD-13361 | EMD-13362 | EMD-13358 | EMD-13357 | EMD-13356 | EMD-13369 | EMD-13368 | EMD-13367 | EMD-13366 | EMD-13365 | EMD-13363 | |
| PDB 7PEW | PDB 7PEX | PDB 7PEY | PDB 7PEZ | PDB 7PEV | PDB 7PEU | PDB 7PET | PDB 7PF6 | PDB 7PF5 | PDB 7PF4 | PDB 7PF3 | PDB 7PF2 | PDB 7PF0 | |
| Data collection and processing | |||||||||||||
| Magnification | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 60 | 60 | 60 | 60 | 60 | 60 | 60 | 60 | 60 | 60 | 60 | 60 | 60 |
| Defocus range (μm) | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 |
| Pixel size (Å/pix) | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 | 1.05 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
| Initial particle images | 1,341,160 | 1,341,160 | 1,341,160 | 1,341,160 | 1,341,160 | 1,341,160 | 1,341,160 | 1,259,654 | 1,259,654 | 1,259,654 | 1,259,654 | 1,259,654 | 1,259,654 |
| Final particle images | 174,476 | 128,860 | 174,476 | 20,621 | 174,476 | 174,476 | 20,621 | 110,706 | 61,926 | 110,706 | 51,385 | 110,706 | 27,515 |
| Map resolution (Å) | 4.6 | 5.1 | 4.5 | 7.9 | 6.0 | 7.2 | 9.5 | 4.0 | 3.8 | 4.0 | 4.0 | 5.1 | 11 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 4.2–8.0 | 4.5–7.3 | 4.1–8.7 | 7.2–25 | 4.5–10.8 | 5.6–11 | 6.8–25 | 3.9–11.3 | 3.4–8.1 | 3.8–9.2 | 3.6–9.3 | 4.0–13.0 | 8.0–14 |
| Refinement | |||||||||||||
| Initial models used (PDB code) | 7K5Y | 7K5Y | 7K5Y | 7K5Y | 7K5Y | 75KY | 75KY | 75KY | |||||
| Model resolution (Å) | 4.6 | 5.1 | 4.5 | 7.9 | 6.0 | 7.2 | 9.5 | 4.0 | 3.8 | 4.0 | 4.0 | 5.1 | 11 |
| Model resolution range (Å) | 4.2–8.0 | 4.5–7.3 | 4.1–8.7 | 7.2–25 | 4.5–10.8 | 5.6–11 | 6.8–25 | 3.9–11.3 | 3.4–8.1 | 3.8–9.2 | 3.6–9.3 | 4.0–13.0 | 8.0–14 |
| Map sharpening B factor (Å2) | −150 | −520 | −150 | −300 | −310 | −300 | −500 | 0 | −50 | 0 | −50 | −50 | 0 |
| Model composition | |||||||||||||
| Non-hydrogen atoms | 13,304 | 13, 880 | 13,099 | 14,058 | 26,403 | 40,119 | 54,040 | 13,470 | 13,470 | 12,935 | 13,470 | 36,610 | 41,515 |
| Protein residues | 768 | 843 | 768 | 843 | 1,536 | 2,379 | 3,222 | 843 | 843 | 768 | 843 | 1,611 | 2,454 |
| DNA | 352 | 354 | 342 | 364 | 694 | 1040 | 1396 | 334 | 334 | 334 | 334 | 678 | 1,082 |
| B factors (Å2) | |||||||||||||
| Protein | 224 | 140 | 252 | 373 | 252 | 203 | 248 | 180 | 152 | 158 | 178 | 217 | 163 |
| DNA | 294 | 191 | 315 | 419 | 372 | 302 | 220 | 222 | 190 | 241 | 220 | 325 | 340 |
| R.m.s. deviations | |||||||||||||
| Bond lengths (Å) | 0.006 | 0.005 | 0.006 | 0.006 | 0.006 | 0.006 | 0.007 | 0.008 | 0.006 | 0.005 | 0.007 | 0.007 | 0.011 |
| Bond angles (°) | 0.912 | 0.932 | 0.895 | 0.910 | 0.957 | 1.087 | 1.280 | 1.054 | 0.889 | 0.887 | 0.944 | 0.974 | 1.335 |
| Validation | |||||||||||||
| MolProbity score | 1.3 | 1.36 | 1.14 | 1.46 | 1.45 | 1.42 | 1.64 | 1.62 | 1.32 | 1.41 | 1.43 | 1.47 | 1.56 |
| Clashscore | 5.53 | 6.47 | 7.45 | 8.54 | 8.22 | 7.70 | 13.62 | 9.20 | 5.86 | 5.99 | 6.15 | 8.76 | 9.13 |
| Poor rotamers (%) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| Ramachandran plot | |||||||||||||
| Favored (%) | 98.9 | 98.4 | 98.4 | 98.2 | 98.4 | 98.6 | 98.4 | 97.3 | 98.2 | 97.6 | 97.6 | 98.2 | 97.7 |
| Allowed (%) | 1.1 | 1.6 | 1.6 | 1.8 | 1.6 | 1.4 | 1.6 | 2.7 | 1.8 | 2.4 | 2.4 | 1.8 | 2.3 |
| Disallowed (%) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
Nuc 1, 2 and 3 refer to nucleosome 1, 2 and 3; stack refers to stacked nucleosomes 1 and 3; trinuc refers to the trinucleosome consisting of nucleosomes 1, 2 and 3; tetranuc refers to the tetranucleosome.