Table1.
Cryo-EM data collection, refinement, and validation statistics
| Open-Na260, TMD-STG (EMDB-29386) (PDB 8FQF) | Open-CaNaMg, TMD-STG (EMDB-29360) (PDB 8FP9) | Open-Ca150, TMD-STG (EMBD-29737) (PDB 8FQ1) | Open-Na610, TMD-STG (EMDB-29359) (PDB 8FP4) | Open-Ca10, TMD-STG (EMDB-29382) (PDB 8FQB) | Open-Na110, TMD-STG (EMBD-29378) (PDB 8FQ5) | Open-CaNaMg/N619K, TMD-STG (EMDB-29369) (PDB 8FPS) | Closed-CaNaMg, TMD-STG (EMDB-29363) (PDB 8FPG) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Data collection and processing | ||||||||||||||||
| Magnification | 105,000x | 130,000x | 130,000x | 105,000x | 130,000x | 130,000x | 130,000x | 130,000x | ||||||||
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 | ||||||||
| Electron exposure (e−/Å2) | 51 | 50 | 50 | 50 | 53 | 52 | 54.6 | 56 | ||||||||
| Defocus range (μm) | −0.7 to −2.1 | −0.5 to −1.5 | −0.8 to −2.0 | −0.8 to −2.0 | −0.8 to −2.0 | −0.6 to −2.0 | −0.8 to −2.0 | −0.8 to −1.8 | ||||||||
| Pixel size (Å) | 0.820 | 0.8195# | 0.8195# | 0.820 | 0.8195# | 0.8195# | 0.8195# | 0.8195# | ||||||||
| Energy filter band width (eV) | 20 | 15 | 20 | 20 | 20 | 20 | 20 | 15 | ||||||||
| Number of micrographs | 16,096 | 32,662 | 28,472 | 23,493 | 28,505 | 30,384 | 34,729 | 34,553 | ||||||||
| Initial particle images (no.) | 5,409,247 | 5,075,710 | 5,573,868 | 5,140,390 | 7,059,177 | 4,655,266 | 6,655,184 | 3,905,978 | ||||||||
| Final particle images (no.) | 1,093,405 | 822,038 | 540,796 | 901,154 | 986,075 | 692,680 | 693,935 | 847,436 | ||||||||
| Symmetry imposed | C1 | C2 | C1 | C2 | C1 | C2 | C1 | C2 | C1 | C2 | C1 | C2 | C1 | C2 | C1 | C2 |
| Map resolution (Å) | 2.38 | 2.29 | 2.59 | 2.44 | 2.78 | 2.59 | 2.50 | 2.40 | 2.48 | 2.36 | 2.42 | 2.34 | 2.50 | 2.38 | 2.42 | 2.32 |
| Map resolution with LBD* (Å) | 2.50 | n.d. | 2.63 | 2.57 | 2.84 | 2.73 | 2.57 | 2.46 | 2.52 | 2.44 | 2.46 | 2.38 | 2.59 | 2.48 | 2.52 | n.d. |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.3-3.7 | 2.2-3.5 | 2.5-4.1 | 2.4-3.8 | 2.6-4.3 | 2.5-4.1 | 2.4-3.9 | 2.3-3.9 | 2.4-4.1 | 2.3-3.9 | 2.3-4.0 | 2.2-3.7 | 2.4-4.2 | 2.3-3.9 | 2.3-3.9 | 2.2-3.7 |
| Refinement (C2) ^ | ||||||||||||||||
| Initial model used (PDB code) | 5WEO | 5WEO | 5WEO | 5WEO | 5WEO | 5WEO | 5WEO | 5WEO | ||||||||
| Model resolution (Å) | 2.0/2.3 (masked) | 2.2/2.5 (masked) | 2.2/2.7 (masked) | 2.2/2.4 (masked) | 2.1/2.5 (masked) | 2.1/2.4 (masked) | 1.9/2.6 (masked) | 2.0/2.4 (masked) | ||||||||
| FSC threshold | 0.143/0.5 | 0.143/0.5 | 0.143/0.5 | 0.143/0.5 | 0.143/0.5 | 0.143/0.5 | 0.143/0.5 | 0.143/0.5 | ||||||||
| Map sharpening B factor (Å2) | −56.0 | −69.5 | −72.1 | −70.8 | −64.9 | −58.3 | −62.8 | −62.0 | ||||||||
| Model composition | ||||||||||||||||
| Non-hydrogen atoms | 10,895 | 10,851 | 10,876 | 10,876 | 10,823 | 10,876 | 10,602 | 10,674 | ||||||||
| Protein residues | 1,366 | 1,366 | 1,366 | 1,366 | 1,366 | 1,366 | 1,338 | 1,348 | ||||||||
| Ligands | CL:2 | CA:1, CL:4 | CA:2 | CL:2 | CA:1, CL:2 | CL:4 | CL:4 | CL:4 | ||||||||
| Water | 231 | 190 | 170 | 218 | 176 | 220 | 152 | 187 | ||||||||
| B factors (Å2) | ||||||||||||||||
| Protein | 38.03 | 57.87 | 55.01 | 40.64 | 41.01 | 39.99 | 35.33 | 42.86 | ||||||||
| Ligand | 59.77 | 76.98 | 87.40 | 73.02 | 75.39 | 63.98 | 66.30 | 71.43 | ||||||||
| Water | 25.84 | 44.19 | 45.02 | 36.14 | 33.39 | 37.15 | 27.41 | 38.77 | ||||||||
| R.m.s. deviations | ||||||||||||||||
| Bond lengths (Å) | 0.002 | 0.002 | 0.002 | 0.002 | 0.002 | 0.002 | 0.002 | 0.003 | ||||||||
| Bond angles (°) | 0.428 | 0.478 | 0.403 | 0.421 | 0.451 | 0.441 | 0.370 | 0.489 | ||||||||
| Validation | ||||||||||||||||
| MolProbity score | 1.30 | 1.13 | 1.21 | 1.36 | 1.45 | 1.23 | 1.12 | 1.73 | ||||||||
| Clashscore | 4.62 | 3.35 | 3.70 | 4.15 | 4.96 | 3.44 | 3.32 | 4.90 | ||||||||
| Poor rotamers (%) | 0.54 | 0.98 | 1.17 | 1.25 | 1.79 | 1.16 | 1.01 | 1.84 | ||||||||
| Ramachandran plot | ||||||||||||||||
| Favored (%) | 97.72 | 98.03 | 98.01 | 97.57 | 98.10 | 97.80 | 98.76 | 96.00 | ||||||||
| Allowed (%) | 2.28 | 1.97 | 1.99 | 2.43 | 1.90 | 2.20 | 1.24 | 4.00 | ||||||||
| Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | ||||||||
#
The pixel size (Å) was 0.647 at the detector level prior to binning
*
Resolution of the map generated by focused refinement of the LBD-TMD-STG
^
Model refinement was conducted against the C2 map of TMD-STG
n.d. Not determined