Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structure of the transcribing RNA polymerase II–Elongin complex
Map 5 Elongin focused (EMD-16830) | Map 6 Pol II core focused (EMD-16831) | Map 7 stalk focused (EMD-16832) | Map 10 SPT6 global (EMD-16833) | Map 11 SPT6 focused (EMD-16834) | Map12 Elongin global (EMD -16836) | Map 14 Pol II–SPT6 global (EMD-16828) | Map 15 Pol II–SPT6 focused (EMD-16829) | |
|---|---|---|---|---|---|---|---|---|
Data collection and processing | ||||||||
Magnification | ×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 |
Electron exposure (e–/Å2) | 40.09 | 40.09 | 40.09 | 40.09 | 40.09 | 40.09 | 40.09 | 40.09 |
Defocus range (μm) | 0.35–7.50 | 0.35–7.50 | 0.35–7.50 | 0.35–7.50 | 0.35–7.50 | 0.35–7.50 | 0.35–7.50 | 0.35–7.50 |
Pixel size (Å) | 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 |
Initial particle images (no.) | 177,945 | 177,945 | 177,945 | 177,945 | 177,945 | 318,472 | 896,636 | 896,636 |
Final particle images (no.) | 136,189 | 136,189 | 136,189 | 118,642 | 118,642 | 72,087 | 174,029 | 174,029 |
Map resolution (Å) | 3.61 | 2.69 | 3.67 | 2.86 | 4.2 | 3.05 | 3.04 | 3.64 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | N/A | N/A | N/A | 2.61–13.2 | N/A | 2.71–15.0 | N/A | |
Map sharpening B factor (Å2) | −124.0 | −48.4 | −103.3 | −55.9 | −123.7 | −49.2 | −103.3 | −168.5 |
Refinement map | Composite map 1 (EMD-16838) | Composite map 2 (EMD-16837) | Local resolution filtered map 12 (EMD-16840) | Composite map 3 (EMD-16835) | ||||
Current model | Structure 2 (PDB 8OEW) | Structure 3 (PDB 8OEV) | Structure 1 (PDB 8OF0) | Structure 4 (PDB 8OEU) | ||||
Initial model used (PDB code) | 7OKX (Pol II), AlphaFold2 (ELOA–ELOB–ELOC complex) | Structure 2 (this study), 7OOP (SPT6) | Structure 2 (this study) | Structure 2 (this study), 7OOP (SPT6) | ||||
Model resolution (Å) | 2.80 | 2.80 | 3.0 | 3.00 | ||||
FSC threshold | 0.50 | 0.50 | 0.5 | 0.50 | ||||
Model–map correlation coefficients CC (masked) | 0.82 | 0.77 | 0.82 | 0.77 | ||||
Model composition | ||||||||
Non-hydrogen atoms | 35,037 | 41,781 | 41,700 | 39,225 | ||||
Protein residues | 4,180 | 5,005 | 5,010 | 4,683 | ||||
Nucleotides | 77 | 77 | 75 | 79 | ||||
Ligands | 9 | 9 | 9 | 9 | ||||
B factors (Å2) | ||||||||
Protein | 39.38 | 49.03 | 71.22 | 65.51 | ||||
Nucleotides | 131.58 | 131.58 | 176.27 | 212.48 | ||||
Ligand | 83.18 | 83.18 | 110.64 | 102.34 | ||||
R.m.s. deviations | ||||||||
Bond lengths (Å) | 0.005 | 0.005 | 0.006 | 0.006 | ||||
Bond angles (°) | 0.775 | 1.101 | 1.124 | 0.876 | ||||
Validation | ||||||||
MolProbity score | 1.54 | 1.70 | 1.69 | 1.57 | ||||
Clashscore | 6.09 | 8.88 | 8.05 | 6.60 | ||||
Poor rotamers (%) | 0 | 0 | 0.02 | 0 | ||||
Ramachandran plot | ||||||||
Favored (%) | 96.68 | 96.55 | 96.31 | 96.75 | ||||
Allowed (%) | 3.32 | 3.45 | 3.69 | 3.25 | ||||
Disallowed (%) | 0 | 0 | 0 | 0 | ||||
