| Dataset . | SP1 untreated . | SP2 EDTA treated . | SP3sym EDTA treated . | SP3bent EDTA treated . | SP4sym EDTA/TPEN treated . | SP4bent EDTA/TPEN treated . |
|---|---|---|---|---|---|---|
| Deposition | N/A | N/A | N/A | N/A | ||
| PDB | 7KZX | 7KZZ | ||||
| EMDB | EMD-23092 | EMD-23093 | ||||
| Data collection and processing | ||||||
| Magnification | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 83 | 77 | 65 | 65 | 50 | 50 |
| Defocus range (μm) | 1.0-3.0 | 1.5-3.0 | 1-2.5 | 1-2.5 | 1-2.5 | 1-2.5 |
| Pixel size (Å) | 1.035 | 1.035 | 1.048 | 1.048 | 1.079 | 1.079 |
| Symmetry imposed | C2 | C1 | C2 | C1 | C2 | C1 |
| Initial particle images (no.) | 473,960 | 848,576 | 1,448,191 | 1,448,191 | 1,685,559 | 1,685,559 |
| Final particle images (no.) | 102,390 | 140,565 | 151,898 | 85,207 | 287,608 | 140,971 |
| Map resolution (Å) | 3.83 | 4.00 | 3.42 | 4.18 | 3.52 | 4.66 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Model refinement | MDFFa | MDFFa | MDFFa | |||
| Model composition | ||||||
| Nonhydrogen atoms | 10416 | 10446 | 10470 | 10446 | 10468 | 10446 |
| Protein residues | 1362 | 1361 | 1364 | 1361 | 1364 | 1361 |
| Ligands | 8 | 0 | 8 | 0 | 0 | 0 |
| RMS deviations | ||||||
| Bond lengths (Å) | 0.004 | 0.011 | 0.014 | 0.012 | 0.012 | 0.009 |
| Bond angles (°) | 0.884 | 1.103 | 2.397 | 1.275 | 1.238 | 1.119 |
| Validation | ||||||
| MolProbity score | 2.39 | 2.31 | 2.13 | 2.73 | 2.41 | 2.65 |
| Clashscore | 20.96 | 19.88 | 2.30 | 40.62 | 21.56 | 34.86 |
| Rotamer outliers (%) | 0.00 | 0.00 | 4.11 | 0.00 | 0.00 | 0.00 |
| CaBLAM outliers (%) | 3.88 | 4.72 | 5.70 | 6.02 | 5.02 | 4.42 |
| Ramachandran plot | ||||||
| Favored (%) | 89.16 | 91.10 | 85.00 | 86.16 | 88.66 | 86.84 |
| Allowed (%) | 10.84 | 8.60 | 11.57 | 13.61 | 11.04 | 13.16 |
| Disallowed (%) | 0.00 | 0.30 | 3.43 | 0.22 | 0.30 | 0.00 |
| Model vs. data CC (mask) | 0.78 | 0.81 | 0.78 | 0.78 | 0.81 | 0.82 |
| Dataset . | SP1 untreated . | SP2 EDTA treated . | SP3sym EDTA treated . | SP3bent EDTA treated . | SP4sym EDTA/TPEN treated . | SP4bent EDTA/TPEN treated . |
|---|---|---|---|---|---|---|
| Deposition | N/A | N/A | N/A | N/A | ||
| PDB | 7KZX | 7KZZ | ||||
| EMDB | EMD-23092 | EMD-23093 | ||||
| Data collection and processing | ||||||
| Magnification | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 |
| Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 83 | 77 | 65 | 65 | 50 | 50 |
| Defocus range (μm) | 1.0-3.0 | 1.5-3.0 | 1-2.5 | 1-2.5 | 1-2.5 | 1-2.5 |
| Pixel size (Å) | 1.035 | 1.035 | 1.048 | 1.048 | 1.079 | 1.079 |
| Symmetry imposed | C2 | C1 | C2 | C1 | C2 | C1 |
| Initial particle images (no.) | 473,960 | 848,576 | 1,448,191 | 1,448,191 | 1,685,559 | 1,685,559 |
| Final particle images (no.) | 102,390 | 140,565 | 151,898 | 85,207 | 287,608 | 140,971 |
| Map resolution (Å) | 3.83 | 4.00 | 3.42 | 4.18 | 3.52 | 4.66 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Model refinement | MDFFa | MDFFa | MDFFa | |||
| Model composition | ||||||
| Nonhydrogen atoms | 10416 | 10446 | 10470 | 10446 | 10468 | 10446 |
| Protein residues | 1362 | 1361 | 1364 | 1361 | 1364 | 1361 |
| Ligands | 8 | 0 | 8 | 0 | 0 | 0 |
| RMS deviations | ||||||
| Bond lengths (Å) | 0.004 | 0.011 | 0.014 | 0.012 | 0.012 | 0.009 |
| Bond angles (°) | 0.884 | 1.103 | 2.397 | 1.275 | 1.238 | 1.119 |
| Validation | ||||||
| MolProbity score | 2.39 | 2.31 | 2.13 | 2.73 | 2.41 | 2.65 |
| Clashscore | 20.96 | 19.88 | 2.30 | 40.62 | 21.56 | 34.86 |
| Rotamer outliers (%) | 0.00 | 0.00 | 4.11 | 0.00 | 0.00 | 0.00 |
| CaBLAM outliers (%) | 3.88 | 4.72 | 5.70 | 6.02 | 5.02 | 4.42 |
| Ramachandran plot | ||||||
| Favored (%) | 89.16 | 91.10 | 85.00 | 86.16 | 88.66 | 86.84 |
| Allowed (%) | 10.84 | 8.60 | 11.57 | 13.61 | 11.04 | 13.16 |
| Disallowed (%) | 0.00 | 0.30 | 3.43 | 0.22 | 0.30 | 0.00 |
| Model vs. data CC (mask) | 0.78 | 0.81 | 0.78 | 0.78 | 0.81 | 0.82 |
FSC, forward scatter.
Models created by Namdinator, which removes Zn ligands during its fitting process.