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. 2022 Apr 21;29(5):420–429. doi: 10.1038/s41594-022-00755-1

Table 1.

Cryo-EM data collection, refinement and validation statistics

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 (e2) 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