Table 1.
Closed, consensus (EMD-12605) (PDB 7NVL) | Closed, tubulin-bound (EMD-12607) (PDB 7NVN) | Closed, Actin/PhLP2A-bound (EMD-12606) (PDB 7NVM) | Open (EMD-12608) (PDB 7NVO) | Open, Map-only (EMD-13754) | |
---|---|---|---|---|---|
Data collection and processing | |||||
Magnification | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 62 | 62 | 62 | 62 | 62 |
Defocus range (μm) | 0.75 to 2.5 | 0.75 to 2.5 | 0.75 to 2.5 | 0.75 to 2.5 | 0.75 to 2.5 |
Pixel size (Å) | 1.06 | 1.06 | 1.06 | 1.06 | 1.06 |
Symmetry imposed | C2 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 3,856,544 | 3,856,544 | 3,856,544 | 3,856,544 | 3,856,544 |
Final particle images (no.) | 316,195 | 93,758 | 63,082 | 50,405 | 144,903 |
Map resolution (Å) | 2.5 | 3.0 | 3.1 | 3.5 | 3.5 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 2.5–4.4 | 2.8–4.8 | 2.9–6.6 | 3.2–9.9 | 3.1–11.7 |
Map sharpening B factor (Å2) | -63.0 | -65.3 | −57.7 | −70.2 | −95.3 |
Refinement | |||||
Initial model used (PDB code) | 6KS6 | 6KS6 | 6KS6 | 6NRA | |
Model-to-map resolution (Å) | 2.64 | 3.05 | 3.27 | 3.51 | |
FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | |
Model-to-map correlation (Phenix) | 0.73 | 0.86 | 0.74 | 0.81 | |
Model composition | |||||
Non-hydrogen atoms | 66,477 | 69,139 | 71,009 | 34,246 | |
Protein residues | 8626 | 8970 | 9219 | 4480 | |
Ligands | 48 | 48 | 48 | 44 | |
B factors (Å2) | |||||
Protein | 72.62 | 72.55 | 70.77 | 64.35 | |
Ligand | 171.45 | 171.45 | 158.28 | 136.15 | |
R.m.s. deviations | |||||
Bond lengths (Å) | 0.007 | 0.004 | 0.008 | 0.005 | |
Bond angles (°) | 0.827 | 0.607 | 0.863 | 0.816 | |
Validation | |||||
MolProbity score | 1.64 | 1.77 | 1.85 | 2.07 | |
Clash score | 4.63 | 6.80 | 7.32 | 6.81 | |
Poor rotamers (%) | 1.73 | 1.75 | 1.55 | 1.87 | |
Ramachandran plot | |||||
Favored (%) | 96.57 | 96.69 | 95.6 | 92.01 | |
Allowed (%) | 3.33 | 3.22 | 4.29 | 7.81 | |
Disallowed (%) | 0.09 | 0.09 | 0.11 | 0.18 |