Table 1 Cryo-EM data collection, refinement, and validation statistics
From: Structure and function of the human apoptotic scramblase Xkr4
Human Xkr4 (EMDB- 44744) (PDB 9BOJ) | |
|---|---|
Data collection and processing | |
Magnification | 105,000 |
Voltage (kV) | 300 |
Electron exposure (e–/Å2) | 58.28 |
Defocus range (μm) | 0.9–2.6 |
Pixel size (Å) | 0.825 |
Symmetry imposed | C1 |
Initial particle images (no.) | 5,540,840 |
Final particle images (no.) | 305,611 |
Map resolution (Å) FSC threshold | 3.45 0.143 |
Map resolution range (Å) | 3.0-4.6 |
Refinement | |
Initial model used (PDB code) | N/A |
Model resolution (Å) FSC threshold | 3.4 0.143 |
Model resolution range (Å) | 3.2–3.6 |
Map sharpening B factor (Å2) | −150 |
Model composition Non-hydrogen atoms Protein residues Ligands | 2551 321 0 |
B factors (Å2) Protein Ligand | 9.91//104.94/45.57(min/max/mean) N/A |
R.m.s. deviations Bond lengths (Å) Bond angles (°) | 0.003 0.489 |
Validation MolProbity score Clashscore Poor rotamers (%) | 2.39 4.60 8.33 |
Ramachandran plot Favored (%) Allowed (%) Disallowed (%) | 92.70 7.30 0 |
