Table 1. Data collection, refinement, and validation statistics.
| Holocomplex at low [Ca2+] PDB: 6XQN EMDB: EMD-22290 |
Ca2+-bound MICU1-MICU2 PDB: 6XQO EMDB: EMD-22291 |
|
|---|---|---|
| Data collection and processing | ||
| Microscope | FEI Titan Krios (at MSKCC) | FEI Titan Krios (at MSKCC) |
| Camera | Gatan K3 | Gatan K3 |
| Magnification | 22,500× | 22,500× |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e–/Å2) | 71 | 71 |
| Defocus range (μm) | −1.0 ~ −3.0 | −0.8 ~ −2.3 |
| Pixel size (Å) | 1.064 (0.532)* | 1.064 (0.532)* |
| Software | RELION 3.0, cryoSPARC v2 | RELION 3.0, cryoSPARC v2 |
| Symmetry imposed | C1 | C1 |
| Initial particle images (no.) | 17,440,131 | 4,397,598 |
| Final particle images (no.) | 350,160 | 115,687 |
| Overall map resolution (Å) FSC threshold 0.143 |
3.3 | 3.1 |
| Local map resolution range (Å) | 3.0–5.0 | 2.8–5.0 |
| Refinement | ||
| Software | Phenix 1.13 real-space-refine | Phenix 1.13 real-space-refine |
| Initial model used (PDB code) | N/A | N/A |
| Model resolution (Å) FSC threshold 0.5 |
3.6 | 3.5 |
| Map sharpening B factor (Å2) | −77 | −38 |
| Model composition | ||
| Non-hydrogen atoms | 9433 | 4225 |
| Protein residues | 1290 | 566 |
| Ligands | 1 (Calcium ion) | 4 (Calcium ions) |
| Water | 0 | 0 |
| B factors (Å2) | ||
| Protein | 124.29 | 88.3 |
| Ligand | 70.1 | 94.9 |
| R.m.s. deviations | ||
| Bond lengths (Å) | 0.006 | 0.004 |
| Bond angles (°) | 1.027 | 0.569 |
| Validation | ||
| MolProbity score | 1.85 | 2.25 |
| Clashscore | 7.13 | 10.75 |
| Ramachandran plot | ||
| Favored (%) | 97.45 | 95.65 |
| Allowed (%) | 2.55 | 4.35 |
| Disallowed (%) | 0.0 | 0.0 |
| *Super-resolution pixel size. |