Table 1.
WT declination | WT declination + CPSF6-FG | T = 1 (CA-G60A G61P) | T = 1 (CA-M66A) | T = 1 (CA-G60A G61P M66A) | ||
---|---|---|---|---|---|---|
EMDB | EMD-26715 | EMD-28186 | EMD-28054 | EMD-28057 | EMD-26718 | |
PDB | 7URN | 8EJL | 8EEP | 8EET | 7URT | |
Data collection, processing and map calculation | ||||||
Magnification | ×81,000 | ×81,000 | ×81,000 | ×92,000 | ×81,000 | |
Voltage (kV) | 300 | 300 | 300 | 200 | 300 | |
Electron exposure (e–/Å2) | 50 | 54 | 50 | 48 | 50 | |
Defocus range (μm) | 0.5 to 2.5 | 0.75 to 2.5 | 0.5 to 2.5 | 0.5 to 2.5 | 0.5 to 2.5 | |
Pixel size (Å) | 1.08 | 1.08 | 1.08 | 0.75 | 1.08 | |
Symmetry imposed | C5 | C5 | I | I | I | |
Particles | 525,219 | 166,463 | 494,057 | 116,627 | 509,666 | |
Map resolution (Å) | 3.4 | 3.9 | 2.2 | 3.1 | 2.4 | |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | |
Map resolution range (Å) | 2.3–8.3 | 2.5–8.9 | 2.2–4.9 | 2.1–7.2 | 2.4–5.2 | |
Coordinate modeling and refinement | ||||||
Chain A (pentamer) | Chains L,M,N (half-hexamer) | |||||
Initial model | PDB 4XFX | PDB 4XFX | PDB 7URN | PDB 7URT | PDB 7URT | PDB 4XFX |
Model resolution (Å) | 3.4 | 3.6 | 4.1 | 2.5 | 3.4 | 2.5 |
FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
Map sharpening B-factor (Å2) | 146.9 | 146.9 | 159.3 | 97.0 | 144.4 | 109.7 |
Model composition | ||||||
Non-hydrogen atoms | 1,725 | 5,175 | 4,431 | 1,726 | 1,726 | 1,726 |
Protein residues | 221 | 663 | 619 | 221 | 221 | 221 |
IP6 | 2 | 0 | 0 | 2 | 2 | 2 |
B-factors (Å2) | 73.2 | 78.8 | 117.0 | 42.9 | 42.6 | |
Root mean squared deviations | ||||||
Bond lengths (Å) | 0.006 | 0.004 | 0.005 | 0.002 | 0.004 | 0.004 |
Bond angles (°) | 0.623 | 0.508 | 0.545 | 0.647 | 1.019 | 0.554 |
Validation | ||||||
MolProbity score | 1.57 | 1.42 | 1.81 | 1.33 | 1.37 | 1.34 |
Clash score | 8.40 | 5.79 | 7.23 | 3.95 | 6.23 | 4.05 |
Poor rotamers (%) | 0.43 | 1.24 | 3.04 | 1.59 | 1.07 | 1.60 |
Ramachandran plot | ||||||
Favored (%) | 97.26 | 97.87 | 97.82 | 100 | 99.54 | 99.09 |
Outliers (%) | 0 | 0 | 0 | 0 | 0 | 0 |
Z-score | 1.00 | 1.79 | 1.74 | 1.98 | 1.87 | 1.22 |