Table 2. Cryo-EM data collection, refinement and validation statistics of the Ca2+ bound nhTMEM16 in nanodiscs.
| nhTMEM16, 2N2, +Ca2+open (EMDB-4592, PDB 6QM9) |
nhTMEM16, 2N2, +Ca2+intermediate closed (EMDB-4593, PDB 6QMA) |
nhTMEM16, 2N2, +Ca2+closed (EMDB-4594, PDB 6QMB) |
|
|---|---|---|---|
| Data collection and processing | |||
| Microscope Camera Magnification |
FEI Talos Arctica Gatan K2 Summit + GIF 49,407 |
||
| Voltage (kV) Exposure time frame/total (s) Number of frames per image |
200 0.15/9 60 |
||
| Electron exposure (e–/Å2) | 52 | ||
| Defocus range (μm) | −0.5 to −2.0 | ||
| Pixel size (Å) Box size (pixels) |
1.012 240 |
||
| Symmetry imposed | C2 | ||
| Initial particle images (no.) | 2,440,110 | ||
| Final particle images (no.) | 71,175 | 33,310 | 41,631 |
| Map resolution (Å) 0.143 FSC threshold |
3.57 |
3.68 |
3.57 |
| Map resolution range (Å) | 3.4–5 | 3.6–5 | 3.4–5 |
| Refinement | |||
| Initial model used | 6QM5 | 6QMB | 6QM5 |
| Model resolution (Å) FSC threshold |
3.6 |
3.7 |
3.6 |
| Model resolution range (Å) | 15–3.6 | 15–3.7 | 15–3.6 |
| Map sharpening B factor (Å2) | −114 | −96 | −95 |
| Model composition Nonhydrogen atoms Protein residues Ligands |
10878 1346 4 |
10714 1324 4 |
10696 1322 4 |
|
B factors (Å2) Protein Ligand |
77.93 54.34 |
84.86 57.57 |
88.53 67.10 |
| R.m.s. deviations Bond lengths (Å) Bond angles (°) |
0.005 0.880 |
0.006 0.872 |
0.008 0.858 |
| Validation MolProbity score Clashscore Poor rotamers (%) |
1.36 3.74 0 |
1.38 4.69 0.18 |
1.42 3.90 0 |
| Ramachandran plot Favored (%) Allowed (%) Disallowed (%) |
96.82 3.18 0 |
97.23 2.77 0 |
96.38 3.62 0 |