Table 1 CryoEM data collection, refinement, and validation statistics.
From: CryoEM structure of the super-constricted two-start dynamin 1 filament
NT14393-32 | NT14393-34 | Combined EMD-11932 PDB-7AX3 | |
|---|---|---|---|
Data collection and processing | |||
Magnification | x130,000 | x130,000 | |
Voltage (kV) | 300 | 300 | |
Electron exposure (e–/Å2) | 45 | 42 | |
Defocus range (μm) | −0.5 to −3 | −1 to −3 | |
Pixel size (Å) | 1.048 | 1.048 | |
Symmetry imposed | C2 helical | C2 helical | C2 helical |
Initial particle images (no.) | 105,404 | 14,722 | 20,938 |
Final particle images (no.) | 13,943 | 6,995 | 16,772 |
Map resolution (Å) | 4.6 | 4.6 | 3.74 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Map sharpening B factor (Å2) | −127.767 | ||
Helical parameters | |||
rise (Å) | 13.58 | ||
twist (°) | 24.43 | ||
Refinement | |||
Initial model used (PDB code) | 6dlu | ||
Model resolution (Å) | 3.4/3.6/3.9 | ||
FSC threshold | 0/0.143/0.5 | ||
Model composition | |||
Non-hydrogen atoms | 169717 | ||
Protein residues | 21037 | ||
Ligands | 36 | ||
GMP-PCP: 36 | |||
Mg: 36 | |||
B factors (Å2) | |||
Protein | 76.07 | ||
Ligand | 72.52 | ||
R.m.s. deviations | |||
Bond lengths (Å) | 0.004 | ||
Bond angles (°) | 0.753 | ||
Validation | |||
MolProbity score | 2.01 | ||
Clashscore | 12.91 | ||
Poor rotamers (%) | 0 | ||
Ramachandran plot | |||
Favored (%) | 94.35 | ||
Allowed (%) | 5.65 | ||
Disallowed (%) | 0 | ||
Rama-Z | |||
whole | 0.87 | ||
helix | 0.19 | ||
sheet | 1.34 | ||
loop | 1.61 | ||
Phenix CC | |||
Mask | 0.81 | ||
Volume | 0.80 | ||
Mean for ligands | 0.87 | ||
