Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structures of transcription preinitiation complex engaged with the +1 nucleosome
PIC–nucleosome, complex A (EMD-14927) (PDB 7ZS9) | PIC–nucleosome, complex B (EMD-14928) (PDB 7ZSA) | PIC–nucleosome, complex C (EMD-14929) (PDB 7ZSB) | |
|---|---|---|---|
Data collection and processing | |||
Magnification | ×81,000 | ×81,000 | ×81,000 |
Voltage (kV) | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 42 | 41 | 45 |
Defocus range (μm) | 0.8 to 2.0 | 0.8 to 2.0 | 0.8 to 2.0 |
Pixel size (Å) | 1.05 | 1.05 | 1.05 |
Symmetry imposed | C1 | C1 | C1 |
Initial particle images (no.) | 2,595,857 | 2,329,133 | 1,410,713 |
Final particle images (no.) | 55,851 | 142,136 | 82,942 |
Map resolution (Å) | 3.3 | 4.0 | 6.6 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 2.4–6.5 | 2.9–7.0 | 3.9–8.4 |
Refinement | |||
Initial models used (PDB code) | |||
Model resolution (Å) | 3.2 | 3.7 | |
FSC threshold | 0.5 | 0.5 | |
Model resolution range (Å) | 2.5–3.3 | 3.0–3.9 | |
Map sharpening B factor (Å2) | −60 | −58 | |
Model composition | |||
Nonhydrogen atoms | 86,362 | 86,373 | |
Protein residues | 9,719 | 9,723 | |
Nucleotides | 418 | 418 | |
Ligands | 19 | 19 | |
B factors (Å2) | |||
Protein | 109.51 | 77.55 | |
Nucleotides | 145.15 | 139.67 | |
Ligand | 150.14 | 111.24 | |
R.m.s. deviations | |||
Bond lengths (Å) | 0.004 | 0.004 | |
Bond angles (°) | 0.687 | 0.753 | |
Validation | |||
MolProbity score | 1.39 | 1.53 | |
Clashscore | 5.48 | 6.62 | |
Poor rotamers (%) | 0.00 | 0.00 | |
Ramachandran plot | |||
Favored (%) | 97.56 | 97.10 | |
Allowed (%) | 2.44 | 2.90 | |
Disallowed (%) | 0.00 | 0.00 | |
