Table 1.
Cryo-EM data collection and refinement statistics
| WT EMD-11234 PDB: 6ZJI |
WT + 30 mM INH EMD-11776 PDB: 7AG8 |
W107R as purified (1 heme) EMD-11625 PDB: 7A2I |
W107R after heme uptake (1 heme) EMD-11677 PDB: 7A7C |
W107R after heme uptake (2 hemes) EMD-11676 PDB: 7A7A |
T275P as purified EMD-11680 PDB: 7A8Z |
T275P after heme uptake EMD-11689 PDB: 7AA3 |
|
|---|---|---|---|---|---|---|---|
| Data collection and processing | |||||||
| Detector | Gatan K2 | Falcon III | Falcon III | Gatan K3 | Gatan K3 | Gatan K2 | Gatan K2 |
| Magnification | 215k | 96k | 92k | 130k | 130k | 130k | 130k |
| Energy filter slit width (eV) | 20 | 20 | 20 | 20 | 20 | 20 | 20 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
| Flux on detector (e/pix/s) | 4.54 | 0.56 | 0.81 | 14.90 | 14.90 | 5.85 | 5.06 |
| Electron exposure on sample (e−/Å2) | 50.29 | 48.60 | 51.30 | 39.30 | 39.30 | 49.40 | 50.60 |
| Target defocus range (μm) | 1.5–2.4 | 0.7–2.1 | 0.7–2.1 | 0.8–1.6 | 0.8–1.6 | 0.8–2.6 | 1.3–2.8 |
| Calibrated pixel size (Å) | 0.64 | 0.83 | 0.83 | 0.652 | 0.652 | 1.05 | 1.05 |
| Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C2 | C2 |
| Extraction box size (pixels) | 360 | 290 | 270 | 380 | 380 | 280 | 290 |
| Initial particle images (no.) | 182,834 | 142,649 | 76,067 | 244,867 | 244,867 | 341,958 | 211,033 |
| Final particle images (no.) | 96,044 | 89,703 | 50,043 | 60,953 | 71,350 | 197,074 | 165,609 |
| Refinement | |||||||
| Map resolution at FSC = 0.143 (Å)∗ | 3.66 | 2.68 | 3.30 | 3.16 | 3.08 | 3.35 | 3.56 |
| Model composition | |||||||
| Non-hydrogen atoms | 10,791 | 10,920 | 9,476 | 9,391 | 10,150 | 8,405 | 8,394 |
| Protein residues | 1,397 | 1,417 | 1,217 | 1,226 | 1,324 | 1,103 | 1,094 |
| B factor (Å2) | |||||||
| Protein | 144.86 | 80.74 | 95.26 | 67.58 | 58.60 | 93.36 | 75.57 |
| Ligand (heme) | 114.89 | 70.76 | 95.03 | 67.09 | 63.95 | – | – |
| RMSD | |||||||
| Bond lengths (Å) | 0.009 | 0.008 | 0.004 | 0.003 | 0.009 | 0.004 | 0.004 |
| Bond angles (°) | 0.813 | 0.699 | 0.609 | 0.523 | 0.744 | 0.575 | 0.647 |
| Validation | |||||||
| MolProbity score | 2.25 | 1.75 | 1.84 | 1.68 | 1.99 | 1.86 | 2.05 |
| Clashscore | 12.85 | 6.61 | 7.20 | 6.62 | 8.88 | 6.97 | 9.36 |
| Poor rotamers (%) | 0.28 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| Ramachandran plot (%) | |||||||
| Favored | 86.50 | 94.26 | 93.15 | 95.54 | 91.02 | 92.34 | 89.85 |
| Allowed | 13.43 | 5.67 | 6.85 | 4.46 | 8.98 | 7.57 | 10.15 |
| Disallowed | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 |
W107R values after heme uptake are from the same data collection. ∗Cryo-EM maps were used to guide model building, final refinement used the gold standard Fourier shell correlation (FSC) = 0.143 maps. All refinement statistics from MolProbity, PHENIX version 1.18.2. RMSD, root-mean-square deviation.