Table 1.
Cryo-EM data collection, refinement and validation statistics
| Empty-pocket 4C (EMDB-41864)(PDB 8U3J) | Empty-pocket 25C (EMDB-41866) (PDB 8U3L) | PI–Br4 consensus (EMDB-41879) (PDB 8U4D) | PI–Br4 conformation 1 (EMDB-41855) (PDB 8U3A) | PI–Br4 conformation 2 (EMDB-41857) (PDB 8U3C) | PIP2–Br4 (EMDB-41873) (PDB 8U43) | DiC8-PIP2 dilated (EMDB-41848) (PDB 8U30) | DiC8-PIP2 closed (EMDB-41847) (PDB 8U2Z) | |
|---|---|---|---|---|---|---|---|---|
| Data collection and processing | ||||||||
| Magnification | 130,000× | 130,000× | 130,000× | 130,000× | 130,000× | 105,000× | 105,000× | 105,000× |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e− Å−2) | 60 | 60 | 47.2 | 47.2 | 47.2 | 45.8 | 45.8 | 45.8 |
| Defocus range (μm) | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 | 0.5–2.0 |
| Pixel size (Å) | 0.68 | 0.68 | 0.644 | 0.644 | 0.644 | 0.835 | 0.835 | 0.835 |
| Symmetry imposed | C4 | C4 | C4 | C1 | C1 | C4 | C4 | C4 |
| Initial particle images (no.) | 5,90,647 | 8,01,469 | 8,08,402 | 8,08,402 | 8,08,402 | 10,89,955 | 37,96,009 | 37,96,009 |
| Final particle images (no.) | 37,836 | 39,183 | 2,63,637 | 7,15,030 | 3,39,518 | 10,89,955 | 2,17,900 | 26,265 |
| Map resolution (Å) | 2.9 | 3.7 | 2.2 | 2.3 | 2.3 | 2.4 | 3 | 3.6 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 2.9–6.0 | 3.5–6.0 | 1.7–6.6 | 2.3–3.0 | 2.3–3.2 | 1.5–6.0 | 3.2–5.5 | 2.8–30 |
| Refinement | ||||||||
| Initial model used (PDB code) | 7MZD | 7MZD | 7L2P | 7L2P | 7L2P | 7L2P | 7MZD | 7L2P |
| Map sharpening B factor (Å2) | NA | NA | NA | −70.5 | −69.9 | −114.7 | −112.4 | −113.5 |
| Model composition | ||||||||
| Nonhydrogen atoms | 17,493 | 17,493 | 18,311 | 3,431 | 3,459 | 18,591 | 17,341 | 17,045 |
| Protein residues | 2,136 | 2,136 | 2,236 | 405 | 405 | 2,224 | 2,112 | 2,040 |
| Ligands | 5 | 5 | 5 | 3 | 4 | 9 | 5 | 13 |
| B factors (min/max/mean Å2) | 34.88/160.73/92.94 | 18.11/125.8/59.01 | 17.01/91.55/48.71 | 34.50/128.78/77.96 | 25.26/49.84/33.92 | 38.70/119.38/76.44 | 24.23/125.10/70.79 | 0.12/109.42/34.69 |
| Protein | 58.52/67.79/58.76 | 29.17/48.73/30.09 | 30.53/31.52/30.79 | 20.00/58.84/38.32 | 20.08/38.76/36.56 | 20.00/63.27/42.00 | 25.45/52.33/32.72 | 9.54/39.93/34.72 |
| Ligand | ||||||||
| Root mean square deviations | ||||||||
| Bond lengths (Å) | 0.28 | 0.28 | 0.29 | 0.38 | 0.39 | 0.32 | 0.28 | 0.3 |
| Bond angles (°) | 0.5 | 0.47 | 0.49 | 0.55 | 0.56 | 0.55 | 0.48 | 0.55 |
| Validation | ||||||||
| MolProbity score | 2 | 2 | 2 | 1.5 | 1 | 1.5 | 2 | 1 |
| Clashscore | 5 | 5 | 2 | 1 | 1 | 1 | 6 | 8 |
| Poor rotamers (%) | 0 | 0 | 5 | 0 | 0 | 4 | 0 | 1 |
| Ramachandran plot | ||||||||
| Favored (%) | 95 | 94 | 94 | 94 | 95 | 94 | 94 | 92 |
| Allowed (%) | 5 | 6 | 6 | 6 | 5 | 6 | 6 | 8 |
| Disallowed (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
NA, not applicable.