Table 2 Statistics of cryo-EM data collection and refinement
From: Amyloid fibril structures link CHCHD10 and CHCHD2 to neurodegeneration
D10-NT-PM1 | D10-NT-PM2 | D10-NT-PM3 | D2-NT | |
|---|---|---|---|---|
PDB ID | 9CWW | 9OYQ | 9OYW | 9OYR |
EMDB ID | EMD-45976 | EMD-71031 | EMD-71037 | EMD-71032 |
Data collection | ||||
Magnification | 64,000 | 100,000 | 64,000 | 105,000 |
Pixel size (Å) | 1.076 | 1.16 | 1.076 | 0.825 |
Defocus Range (μm) | 0.9 to 2.2 | 0.8 to 2.5 | 0.9 to 2.2 | 0.6 to 2.5 |
Voltage (kV) | 300 | 200 | 300 | 300 |
Energy filter | 20 eV | 20 eV | 20 eV | 20 eV |
Microscope/camera | Krios/K3 | Talos Glacios /Falcon 4i | Krios/K3 | Krios/K3 |
Exposure time (s/frame) | 0.05 | 0.127 | 0.05 | 0.045 |
Number of frames | 50 | 50 | 50 | 40 |
Total dose (e−/Å2) | 51.82 | 50 | 51.82 | 48.4 |
Reconstruction | ||||
Micrographs | 8278 | 12,002 | 8278 | 5892 |
Manually picked fibrils | 5167 | 2459 | 5167 | 5435 |
Segments extracted (no.) | 1,902,596 | 415,983 | 1,808,471 | 3,593,244 |
Segments after Class2D (no.) | 667,405 | 351,565 | 47,048 | 63,528 |
Segments after Class3D (no.) | 602,449 | 351,565 | 29,181 | 23,351 |
Crossover used for initial models (Å) | 360 | 680 | 720 | 600 |
Box size for initial model (pixel)a | 384 | 512 | 640 | 896 |
Box size for refinement (pixel)a | 256 | 256 | 256 | 256 |
Resolution (Å) | 2.31 | 2.70 | 2.63 | 2.03 |
Map sharpening B-factor (Å2) | −56.6379 | −70.2058 | −43.8268 | −23.67 |
Symmetry | pseudo-21 | pseudo-21 | C1 | C1 |
Helical rise (Å) | 2.365 | 2.38 | 4.73 | 4.796 |
Helical twist (°) | 178.845 | 179.418 | 1.27 | 1.34 |
Atomic model | ||||
Non-hydrogen atoms | 1272 | 3762 | 5832 | 1664 |
Protein residues | 204 | 612 | 972 | 264 |
Ligands | 0 | 0 | 0 | 0 |
r.m.s.d. Bond lengths | 0.002 | 0.002 | 0.002 | 0.001 |
r.m.s.d. Bond angles | 0.002 | 0.501 | 0.535 | 0.416 |
MolProbity score | 0.825 | 1.27 | 1.88 | 1.48 |
All-atom clashscore | 1.30 | 5.06 | 12.33 | 9.08 |
Rotamer outliers (%) | 5.49 | 0 | 0 | 0 |
Ramachandran Outliers (%) | 0 | 0 | 0 | 0 |
Ramachandran Allowed (%) | 0 | 0 | 4.00 | 0 |
Ramachandran Favored (%) | 100 | 100 | 96.00 | 100 |
S59L D10-NT | T61I D2-NT | R15L D10-NT | |
|---|---|---|---|
PDB ID | 9OYS | 9OYT | 9OYO |
EMDB ID | EMD-71033 | EMD-71034 | EMD-71028 |
Data collection | |||
Magnification | 64,000 | 100,000 | 81,000 |
Pixel size (Å) | 1.076 | 1.16 | 1.083 |
Defocus Range (μm) | 0.8 to 2.5 | 0.8 to 2.5 | 0.5 to 2.5 |
Voltage (kV) | 300 | 200 | 300 |
Energy filter | 20 eV | 20 eV | 20 eV |
Microscope/camera | Krios/K3 | Talos Glacios/Falcon 4i | Krios/K3 |
Exposure time (s/frame) | 0.05 | 0.125 | 0.05 |
Number of frames | 46 | 40 | 40 |
Total dose (e−/Å2) | 59.653 | 40 | 51.21 |
Reconstruction | |||
Micrographs | 4228 | 8291 | 11,144 |
Manually picked fibrils | 1543 | 2459 | 2684 |
Segments extracted (no.) | 658,614 | 1,133,246 | 1,931,884 |
Segments after Class2D (no.) | 61,902 | 315,652 | 152,213 |
Segments after Class3D (no.) | 19,650 | 38,570 | 13,286 |
Crossover used for initial models (Å) | 225 | 430 | 720 |
Box size for initial models (pixel)a | 320 | 448 | 512 |
Box size for refinement (pixel)a | 256 | 256 | 256 |
Resolution (Å) | 3.06 | 3.09 | 3.15 |
Map sharpening B-factor (Å2) | −50.3765 | −62.64 | −64.4635 |
Symmetry | C1 | pseudo-21 | pseudo-21 |
Helical rise (Å) | 4.65 | 2.36 | 2.425 |
Helical twist (°) | 3.88 | 179.04 | 179.3892 |
Atomic model | |||
Non-hydrogen atoms | 1218 | 3834 | 3762 |
Protein residues | 192 | 612 | 612 |
Ligands | 0 | 0 | 0 |
r.m.s.d. Bond lengths | 0.002 | 0.001 | 0.001 |
r.m.s.d. Bond angles | 0.501 | 0.387 | 0.383 |
MolProbity score | 1.42 | 1.82 | 0.97 |
All-atom clashscore | 7.7 | 7.45 | 2.00 |
Rotamer outliers (%) | 0 | 0 | 0 |
Ramachandran Outliers (%) | 0 | 0 | 0 |
Ramachandran Allowed (%) | 1.67 | 6.25 | 0 |
Ramachandran Favored (%) | 98.33 | 93.75 | 100 |
