Table 1 Cryo-EM data collection, refinement, and validation statistics
From: Architecture and activation of human muscle phosphorylase kinase
Inactive_tetramer | Inactive_monomer | Inactive_γδ | Active_tetramer | Active_αγ | |
|---|---|---|---|---|---|
Data collection and processing | |||||
Magnification | 81,000 | 81,000 | |||
Voltage (kV) | 300 | 300 | |||
Electron exposure (e–/Å2) | 60 | 60 | |||
Defocus range (μm) | –1.1 to –1.5 | –1.1 to –1.5 | |||
Pixel size (Å) | 1.07 | 1.07 | |||
Symmetry imposed | C1 | C1 | |||
Initial particle images (no.) | 3,769,745 | 2,434,165 | |||
Final particle images (no.) | 632,973 | 432,047 | |||
Map resolution (Å) | |||||
FSC threshold: 0.143 | 2.92 | 2.72 | 3.12 | 2.94 | 2.91 |
Refinement | |||||
Initial model used (PDB code) | 1CDL | 1CDL | 1CDL | N/A | N/A |
Model resolution (Å) | |||||
FSC threshold: 0.143 | 2.92 | 2.72 | 3.12 | 2.94 | 2.91 |
Map sharpening B factor (Å2) | 71.3 | 70.7 | 86.2 | 83.9 | 76.6 |
Model composition | |||||
Non-hydrogen atoms | 81,428 | 20,357 | 5554 | 65,884 | 8090 |
Protein residues | 10,140 | 2535 | 689 | 8204 | 1018 |
Ligands | 8 | 2 | 1 | 12 | 1 |
B factors (Å2) | |||||
Protein | 110.94 | 57.96 | 79.66 | 91.36 | 49.51 |
Ligand | 138.53 | 96.35 | 72.00 | 99.09 | 77.32 |
R.m.s. deviations | |||||
Bond lengths (Å) | 0.013 | 0.005 | 0.005 | 0.005 | 0.006 |
Bond angles (°) | 1.214 | 1.046 | 1.081 | 1.006 | 1.039 |
Validation | |||||
MolProbity score | 1.57 | 1.35 | 1.48 | 1.53 | 1.52 |
Clashscore | 7.61 | 6.29 | 6.14 | 5.95 | 5.30 |
Poor rotamers (%) | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 |
Ramachandran plot | |||||
Favored (%) | 97.16 | 97.97 | 97.22 | 96.78 | 96.39 |
Allowed (%) | 2.83 | 2.03 | 2.78 | 3.22 | 3.61 |
Disallowed (%) | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 |
