Table 1.
Cryo-EM data collection, refinement and validation statistics
| No. 1 IMPDH1(514) extended filament (interface) (EMDB 24437) (PDB 7RER) | No. 2 IMPDH1(514) extended filament (octamer) (EMDB 24438) (PDB 7RES) | No. 3 IMPDH1(514) compressed filament (interface) (EMDB 24439) (PDB 7RFE) | No. 4 IMPDH1(514) compressed filament (octamer) (EMDB 24441) (PDB 7RFG) | No. 5 IMPDH1(546) extended filament (interface) (EMDB 24451) (PDB 7RGL) | No. 6 IMPDH1(546) extended filament (octamer) (EMDB 24452) (PDB 7RGM) | No. 7 IMPDH1(546) compressed filament (interface) (EMDB 24450) (PDB 7RGI) | No. 8 IMPDH1(546) compressed filament (octamer) (EMDB 24454) (PDB 7RGQ) | No. 9 IMPDH1(595) extended filament (interface) (EMDB 24440) (PDB 7RFF) | No. 10 IMPDH1(595) extended filament (octamer) (EMDB 24442) (PDB 7RFH) | No. 11 IMPDH1(595) compressed filament (interface) (EMDB 24443) (PDB 7RFI) | No. 12 IMPDH1(595) compressed filament (octamer) (EMDB 24448) (PDB 7RGD) | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| Data collection and processing | ||||||||||||
| Microscope | Titan Krios G3 | Titan Krios G3 | Titan Krios G3 | Glacios | Titan Krios G3 | Titan Krios G3 | ||||||
| Camera | Gatan K2 | Gatan K2 | Gatan K3 | Gatan K2 | Gatan K2 | Gatan K3 | ||||||
| Magnification | 130,000 | 130,000 | 130,000 | 130,000 | 130,000 | 130,000 | ||||||
| Voltage (kV) | 300 | 300 | 300 | 200 | 300 | 300 | ||||||
| Electron exposure (e−/Å2) | 90 | 90 | 90 | 90 | 90 | 90 | ||||||
| Defocus range (μm) | −1.5–−3.5 | −0.5–−1.8 | −0.6–−1.8 | −0.5–−3.2 | −0.6–−2.3 | −0.5–−2.5 | ||||||
| Pixel size (Å) | 0.525 | 0.525 | 0.4215 | 1.16 | 0.525 | 0.4215 | ||||||
| Camera mode | super-resolution | super-resolution | super-resolution | counting | super-resolution | super-resolution | ||||||
| Symmetry imposed | D4 | D4 | D4 | D4 | D4 | D4 | D4 | D4 | D4 | D4 | D4 | D4 |
| Initial particle images (no.) | 232,000 | 217,600 | 103,100 | 56,900 | 64,355 | 66,807 | 73,000 | 113,000 | 81,200 | 80,200 | 330,000 | 310,000 |
| Final particle images (no.) | 103,809 | 57,965 | 42,500 | 49,800 | 25,366 | 43,406 | 70,031 | 97,369 | 60,919 | 11,476 | 71,792 | 102,543 |
| Map resolution (Å) | 2.6 | 3.1 | 2.6 | 3.1 | 2.4 | 2.9 | 4.0 | 3.9 | 2.7 | 3.7 | 2.8 | 3.0 |
| 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 |
| Map resolution range (Å) | 2.4–3.4 | 2.8–4.4 | 2.3–3.8 | 2.5–4.5 | 2.4–4.2 | 2.9–5.0 | 3.5–4.6 | 3.5–4.8 | 2.5–4,5 | 3.2–6.0 | 2.6–4.0 | 2.9–4.5 |
| Refinement | ||||||||||||
| Initial model used (PDB code) | 6U8E | 6U8N | 7RER | 7RES | 7RFE | 7RGL | 7RER | 7RES | ||||
| Model resolution (Å) | 3.1 | 2.5 | 2.2 | 2.1 | 1.9 | 2.4 | 3.0 | 3.2 | 2.1 | 3.0 | 2.1 | 2.3 |
| 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 |
| Model resolution range (Å) | inf-3.1 | inf-3.1 | inf-2.6 | inf-3.1 | inf-2.4 | inf-2.9 | inf-4.0 | inf-3.9 | inf-2.7 | inf-3.7 | inf-2.8 | inf-3.0 |
| Map sharpening B factor (Å2) | −87 | −102 | −55 | −52 | −38 | −63 | −137 | −133 | −113 | −93 | −57 | −62 |
| Model composition | ||||||||||||
| Nonhydrogen atoms | 23,504 | 29,056 | 28,568 | 30,584 | 25,528 | 30,192 | 21,960 | 30,288 | 20,400 | 27,538 | 26,496 | 32,584 |
| Protein residues | 3,112 | 3,856 | 3,800 | 3,928 | 3,328 | 3,872 | 2,856 | 3,848 | 2,712 | 3,595 | 3,376 | 4,152 |
| Ligands | IMP (8), NAD+ (8) | IMP (8), NAD+ (8), ATP (16) | IMP (8), ATP (8), GTP (16) | IMP (8), ATP (8), GTP (16) | IMP (8), NAD+ (8) | IMP (8), NAD+ (8), ATP (16) | IMP (8), NAD+ (8) | IMP (8), NAD+ (8), ATP (8) | ATP (16) | IMP (8), NAD+ (8), GTP (16) | IMP (8), NAD+ (8), ATP (8), GTP (16) | |
| B factors (Å2) | ||||||||||||
| Protein | 28.95 | 62.88 | 42.20 | 37.49 | 50.18 | 49.58 | 48.86 | 41.67 | 85.89 | 51.89 | 34.42 | 44.08 |
| Ligand | 31.90 | 67.43 | 58.64 | 45.54 | 48.50 | 55.20 | 55.61 | 54.18 | - | 69.51 | 54.61 | 50.78 |
| R.m.s. deviations | ||||||||||||
| Bond lengths (Å) | 0.58 | 0.011 | 0.019 | 0.018 | 0.009 | 0.019 | 0.015 | 0.020 | 0.011 | 0.016 | 0.021 | 0.020 |
| Bond angles (°) | 0.89 | 1.136 | 2.195 | 2.179 | 1.296 | 1.986 | 1.958 | 2.129 | 1.950 | 2.069 | 2.051 | 2.196 |
| Validation | ||||||||||||
| MolProbity score | 1.72 | 2.54 | 1.44 | 1.34 | 1.85 | 1.75 | 1.57 | 1.82 | 1.41 | 2.13 | 1.60 | 1.87 |
| Clashscore | 7.75 | 11.30 | 1.13 | 1.16 | 3.77 | 1.92 | 2.18 | 2.77 | 1.56 | 4.93 | 3.51 | 2.52 |
| Poor rotamers (%) | 0.7 | 4.87 | 2.97 | 1.91 | 3.66 | 3.63 | 1.62 | 2.39 | 1.97 | 2.73 | 1.61 | 3.22 |
| Ramachandran plot | ||||||||||||
| Favored (%) | 95.72 | 92.96 | 96.24 | 95.64 | 96.18 | 94.56 | 93.80 | 92.63 | 95.90 | 90.17 | 95.63 | 93.08 |
| Allowed (%) | 4.28 | 6.99 | 3.54 | 4.18 | 3.66 | 5.18 | 6.02 | 6.71 | 3.80 | 8.75 | 3.97 | 6.60 |
| Disallowed (%) | 0 | 0.05 | 0.21 | 0.18 | 0.15 | 0.26 | 0.18 | 0.66 | 0.30 | 1.09 | 0.39 | 0.32 |