Extended Data Table 1.
Statistics for cryo-EM data collection, model refinement and validation
| Inward open | Inward semi-occluded | Inward semi-occluded | Fully occluded | |
|---|---|---|---|---|
| Apo LAX3 pH 5.5 | IAA LAX3 pH 7.5 | 2,4-D LAX3 pH 7.5 | 2-NOA LAX3 pH 7.5 | |
| LMNG | LMNG | LMNG | LMNG | |
| Data Collection and processing | ||||
| Microscope | Krios I (eBic) | Krios II (EMBION) | Krios II (EMBION) | Krios II (EMBION) |
| Magnification | 130.000 | 130,000 | 130,000 | 130,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e−/Å2) | 50 | 59.3 and 60.0 | 60.0 | 59.70 |
| Defocus range (μm) | 0.6-2.0 | 0.4-2.6 | 0.4-2.6 | 0.4-2.6 |
| Pixel size (Å) | 0.645 | 0.647 | 0.647 | 0.647 |
| Symmetry imposed | C1 | C1 | C1 | C1 |
| Collected micrographs (no.) | 10.273 | 13,772 and 14,171 | 20.002 | 12.748 |
| Initial particle images (no.) | 5,886,564 | 4,432,384 | 1,470,803 | 3,465,533 |
| Final particle images (no.) | 80.204 | 74.645 | 58.924 | 49.481 |
| Map resolution (Å)* | 3.16 | 3.21 | 3.43 | 2.88 |
| Refinement | ||||
| Initial model used | Alphafold | Alphafold | Alphafold | Alphafold |
| Map sharpening B factor (Å2) | 96.9 | 111.9 | 105.6 | 90.0 |
| Model composition | ||||
| non-hydrogen atoms | 3.132 | 3.311 | 3.312 | 3.396 |
| Protein residues | 393 | 412 | 412 | 420 |
| Ligands | IAC: 1 | CFA: 1 | NOA: 1 | |
| Waters | 0 | 2 | 3 | 8 |
| R.m.s. deviation | ||||
| Bond lenghts (Å) | 0.002 | 0.02 | 0.002 | 0.002 |
| Bond angles (deg) | 0.419 | 0.506 | 0.412 | 0.564 |
| Validation | ||||
| MolProbity score | 1.25 | 1.28 | 1.24 | 1.34 |
| Clashscore | 3.35 | 4.54 | 4.69 | 4.0 |
| Poor rotamers (%) | 0.6 | 0.00 | 0.57 | 0.00 |
| Rama-Z score (Whole/Helix/Loop) | 2.74/2.11/1.01 | 0.45/0.51/0.01 | 2.71/2.26/0.19 | 1.55/1.58/-0.78 |
| CaBLAM score (Outliers/Disfavored/Cα) | 0.54/2.95/0.27 | 1.00/3.75/0.50 | 1.50/5.75/0.50 | 0.97/4.61/0.24 |
| Ramachandran Plot | ||||
| Favored (%) | 97.39 | 97.78 | 98.03 | 97.12 |
| Allowed (%) | 2.61 | 2.22 | 1.97 | 2.88 |
| Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 |
| Deposited model (PDB-ID) | 9QQM | 9H61 | 9H62 | 9H63 |
| Deposited map (EMDB-ID) | 53308 | 51894 | 51895 | 51896 |
Cryo-EM data collection, refinement and validation statistics
* Gold standard FSC with threshold of 0.143
IAC: Indole-3-acetic acid
CFA: 2,4-Dichlorophenoxyacetic acid
NOA: 2-Naphthoxyacetic acid