Cryo-EM data collection, refinement, and validation statistics
| . | IMPDH1(595)-S477D compressed free octamer . | IMPDH1(546)-S477D compressed filament octamer . | IMPDH1(546)-S477D compressed filament interface . | IMPDH1(546)-S477D extended filament octamer . | IMPDH1(546)-S477D extended filament interface . |
|---|---|---|---|---|---|
| Ligands | GTP, ATP, IMP, NAD+ | GTP, ATP, IMP, NAD+ | GTP, ATP, IMP, NAD+ | ATP, IMP, NAD+ | ATP, IMP, NAD+ |
| PDB ID | 8U7M | 8U7Q | 8U7V | 8U8O | 8U8Y |
| EMDB ID | EMD-41986 | EMD-41989 | EMD-42012 | EMD-42026 | EMD-42029 |
| Data collection and refinement | |||||
| Magnification | 36,000 | 36,000 | 36,000 | 105,000 | 105,000 |
| Voltage (kV) | 200 | 200 | 200 | 300 | 300 |
| Electron exposure (e−/Å2) | 65 | 50 | 50 | 50 | 50 |
| Defocus range (µm) | −1.8 to −1.2 | −1.8 to −1.2 | −1.8 to −1.2 | −1.8 to −1.2 | −1.8 to −1.2 |
| Pixel size (data collection) (Å) | 1.16 | 1.16 | 1.16 | 0.4215 | 0.4215 |
| Pixel size (reconstruction) (Å) | 1.16 | 1.16 | 1.16 | 0.843 | 0.843 |
| Micrographs (no.) | 646 | 756 | 756 | 4,632 | 4,632 |
| Initial particles (no.) | 343,619 | 434,369 | 434,369 | 5,836,476 | 5,836,476 |
| Final particles (no.) | 163,814 | 163,916 | 149,184 | 1,773,701 | 1,951,413 |
| Symmetry imposed | D4 | D4 | D4 | D4 | D4 |
| Resolution (CryoSPARC) postprocess (0.143 FSC) (Å) | 3.1 | 3.3 | 3.3 | 2.4 | 2.1 |
| Resolution (3DFSC) (0.5 FSCref) (Å) | 3.2 | 3.4 | 3.5 | 2.4 | 2.3 |
| Model refinement and validation | |||||
| Initial model (PDB ID) | 7RGD | 7RGQ | 7RGI | 7RGM | 7RGL |
| Root-mean-square deviations | |||||
| Bond lengths (Å) | 0.017 | 0.017 | 0.017 | 0.014 | 0.011 |
| Bond angles (°) | 1.378 | 1.334 | 1.412 | 1.302 | 0.989 |
| MolProbity score | 1.79 | 1.60 | 1.66 | 1.44 | 1.30 |
| Clash score | 10.32 | 6.75 | 7.94 | 3.62 | 2.24 |
| C-β deviations | 0% | 0% | 0% | 0% | 0% |
| Rotamer outliers (%) | 0.27% | 0.73% | 0.85% | 1.24% | 1.76% |
| Ramachandran plot | |||||
| Favored (%) | 96.23% | 96.51% | 96.52% | 96.64% | 97.44% |
| Allowed (%) | 3.77% | 3.28% | 3.27% | 3.36% | 2.56% |
| Disallowed (%) | 0% | 0.21% | 0.22% | 0% | 0% |
| Cross-correlation (mask) | 0.69 | 0.83 | 0.83 | 0.75 | 0.86 |
| Map resolution estimates | |||||
| FSC 0.5 (masked) | 3.63 | 3.45 | 3.50 | 2.54 | 2.13 |
| FSC 0.5 (unmasked) | 3.64 | 3.56 | 3.72 | 2.63 | 2.26 |
| . | IMPDH1(595)-S477D compressed free octamer . | IMPDH1(546)-S477D compressed filament octamer . | IMPDH1(546)-S477D compressed filament interface . | IMPDH1(546)-S477D extended filament octamer . | IMPDH1(546)-S477D extended filament interface . |
|---|---|---|---|---|---|
| Ligands | GTP, ATP, IMP, NAD+ | GTP, ATP, IMP, NAD+ | GTP, ATP, IMP, NAD+ | ATP, IMP, NAD+ | ATP, IMP, NAD+ |
| PDB ID | 8U7M | 8U7Q | 8U7V | 8U8O | 8U8Y |
| EMDB ID | EMD-41986 | EMD-41989 | EMD-42012 | EMD-42026 | EMD-42029 |
| Data collection and refinement | |||||
| Magnification | 36,000 | 36,000 | 36,000 | 105,000 | 105,000 |
| Voltage (kV) | 200 | 200 | 200 | 300 | 300 |
| Electron exposure (e−/Å2) | 65 | 50 | 50 | 50 | 50 |
| Defocus range (µm) | −1.8 to −1.2 | −1.8 to −1.2 | −1.8 to −1.2 | −1.8 to −1.2 | −1.8 to −1.2 |
| Pixel size (data collection) (Å) | 1.16 | 1.16 | 1.16 | 0.4215 | 0.4215 |
| Pixel size (reconstruction) (Å) | 1.16 | 1.16 | 1.16 | 0.843 | 0.843 |
| Micrographs (no.) | 646 | 756 | 756 | 4,632 | 4,632 |
| Initial particles (no.) | 343,619 | 434,369 | 434,369 | 5,836,476 | 5,836,476 |
| Final particles (no.) | 163,814 | 163,916 | 149,184 | 1,773,701 | 1,951,413 |
| Symmetry imposed | D4 | D4 | D4 | D4 | D4 |
| Resolution (CryoSPARC) postprocess (0.143 FSC) (Å) | 3.1 | 3.3 | 3.3 | 2.4 | 2.1 |
| Resolution (3DFSC) (0.5 FSCref) (Å) | 3.2 | 3.4 | 3.5 | 2.4 | 2.3 |
| Model refinement and validation | |||||
| Initial model (PDB ID) | 7RGD | 7RGQ | 7RGI | 7RGM | 7RGL |
| Root-mean-square deviations | |||||
| Bond lengths (Å) | 0.017 | 0.017 | 0.017 | 0.014 | 0.011 |
| Bond angles (°) | 1.378 | 1.334 | 1.412 | 1.302 | 0.989 |
| MolProbity score | 1.79 | 1.60 | 1.66 | 1.44 | 1.30 |
| Clash score | 10.32 | 6.75 | 7.94 | 3.62 | 2.24 |
| C-β deviations | 0% | 0% | 0% | 0% | 0% |
| Rotamer outliers (%) | 0.27% | 0.73% | 0.85% | 1.24% | 1.76% |
| Ramachandran plot | |||||
| Favored (%) | 96.23% | 96.51% | 96.52% | 96.64% | 97.44% |
| Allowed (%) | 3.77% | 3.28% | 3.27% | 3.36% | 2.56% |
| Disallowed (%) | 0% | 0.21% | 0.22% | 0% | 0% |
| Cross-correlation (mask) | 0.69 | 0.83 | 0.83 | 0.75 | 0.86 |
| Map resolution estimates | |||||
| FSC 0.5 (masked) | 3.63 | 3.45 | 3.50 | 2.54 | 2.13 |
| FSC 0.5 (unmasked) | 3.64 | 3.56 | 3.72 | 2.63 | 2.26 |