Table 1 Cryo-EM data collection, refinement and validation statistics
From: Hub stability in the calcium calmodulin-dependent protein kinase II
α hub 14-mer | α hub 12-mer | β hub 14-mer | β hub 12-mer | β holoenzyme 14-mer | β holoenzyme open 12-mer | |
|---|---|---|---|---|---|---|
Data collection and processing | ||||||
Magnification | 165,000 | 165,000 | 105,000 | 105,000 | 105,000 | 105,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 60 | 60 | 60 | 60 | 60 | 60 |
Defocus range (μm) | −0.6 to −1.5 | −0.6 to −1.5 | −0.6 to −1.5 | −0.6 to −1.5 | −0.6 to −1.5 | −0.6 to −1.5 |
Pixel size (Å) | 0.74 | 0.74 | 0.86 | 0.86 | 0.86 | 0.86 |
Symmetry imposed | D7 | D6 | D7 | D6 | D7 | C1 |
Initial particle images (no.) | 2,244,235 | 2,024,671 | 2,437,000 | 1,882,694 | 2,074,285 | 2,074,285 |
Final particle images (no.) | 205,902 | 204,506 | 126,970 | 185,091 | 138,904 | 332,360 |
Map resolution (Å) | 2.6 | 2.7 | 2.6 | 2.6 | 3 | 3.5 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 1.9–3.0 | 1.8–3.3 | 1.9–3.0 | 1.9–3.1 | 2.1–3.5 | 2.1–7.9 |
Refinement | ||||||
Initial model used (PDB code) | Alphafold | Alphafold | Alphafold | Alphafold | Alphafold | Alphafold |
Model resolution (Å) | 2.63 | 2.77 | 2.66 | 2.68 | 3.05 | 3.76 |
FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
Map sharpening B factor (Å2) | −127.6 | −124.9 | −102.1 | −99.4 | −119.5 | −111.5 |
Model composition | ||||||
Non-hydrogen atoms | 15,218 | 13,044 | 15,106 | 12,948 | 15,106 | 12,948 |
Protein residues | 1876 | 1608 | 1890 | 1620 | 1890 | 1620 |
Ligands | ||||||
B factors (Å2) | ||||||
Protein | 33.78 | 84.98 | 20.35 | 29.18 | 40.27 | 48.6 |
Ligand | ||||||
R.m.s. deviations | ||||||
Bond lengths (Å) | 0.006 | 0.005 | 0.007 | 0.005 | 0.005 | 0.011 |
Bond angles (°) | 1.993 | 1.439 | 0.87 | 1.336 | 0.703 | 5.564 |
Validation | ||||||
MolProbity score | 0.88 | 1.29 | 1.21 | 1.03 | 2.01 | 1.48 |
Clashscore | 1.13 | 2.49 | 3.6 | 2.43 | 5.18 | 5.68 |
Poor rotamers (%) | 0 | 0 | 0 | 0.87 | 4.35 | 0.87 |
Ramachandran plot | ||||||
Favored (%) | 97.73 | 96.21 | 97.74 | 98.5 | 96.24 | 96.99 |
Allowed (%) | 2.27 | 3.79 | 2.26 | 1.5 | 3.76 | 3.01 |
Disallowed (%) | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
