Table 2 Cryo-EM data collection, refinement and validation statistics
From: Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism
P-Rex1 (N-term) (EMD-25525) | P-Rex1 (C-term) (EMD-25526) | ||
|---|---|---|---|
Data collection and processing | |||
Magnification | ×105,000 | ×105,000 | ×105,000 |
Voltage (kV) | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 51.9 | 51.9 | 51.9 |
Defocus range (μm) | −0.5 to −2.2 | −0.5 to −2.2 | −0.5 to −2.2 |
Pixel size (Å) | 0.823 | 0.823 | 0.823 |
Symmetry imposed | C1 | C1 | C1 |
Initial particle images (no.) | 7,490,128 | 7,490,128 | 7,490,128 |
Final particle images (no.) | 123,896 | 123,896 | 123,896 |
Map resolution (Å) | |||
0.143b/0.5a FSC threshold | 4.2a | 4.4b | 3.4b |
Map resolution range (Å) | |||
0.5 FSC threshold | 3.5 to ~9.0 | 4.0 to ~9.0 | 3.2 to ~6.5 |
Reconstruction type | Consensus | Localized | Localized |
Refinement | |||
Initial model used (PDB code) | |||
Model resolution (Å) | |||
0.143 FSC threshold | 3.5 | 6.7 | 3.2 |
Map sharpening B factor (Å2) | −116 | −101 | −214 |
Model composition | |||
Non-hydrogen atoms | 11,157 | ||
Protein residues | 1,397 | ||
B factors (Å2) | |||
Protein | 138.69 | ||
Root mean squared deviations | |||
Bond lengths (Å) | 0.013 | ||
Bond angles (°) | 1.868 | ||
Validation | |||
MolProbity score | 1.23 | ||
Clash score | 01.52 | ||
Poor rotamers (%) | 1.22 | ||
Ramachandran plot | |||
Favored (%) | 96.09 | ||
Allowed (%) | 3.91 | ||
Disallowed (%) | 0 | ||
