Table 1 Cryo-EM data collection, refinement and validation statistics
Fully recognized PneKC (EMD-37514) (PDB 8WGO) | Pre-binding PneKC (EMD-37337) (PDB 8W7A) | LP-bound PneKC (EMD-37339) (PDB 8W7J) | |
|---|---|---|---|
Data collection and processing | |||
Magnification | 105 k | 105 k | |
Voltage (kV) | 300 | 300 | |
Electron exposure (e–/Å2) | 65.2 | 50 | |
Defocus range (μm) | −1.0 to −2.0 | −1.0 to −2.0 | |
Pixel size (Å) | 0.858 | 0.858 | |
Symmetry imposed | C1 | C1 | |
Initial particle images (no.) | 1,301,086 | 1,272,986 | |
Final particle images (no.) | 133,078 | 179,941 | 143,154 |
Map resolution (Å) | 3.70 | 3.77 | 3.98 |
FSC threshold | 0.143 | 0.143 | 0.143 |
Refinement | |||
Initial model used (PDB code) | AlphaFold2 | 8WGO | 8WGO |
Model resolution (Å) | 4.0 | 4.2 | 4.3 |
FSC threshold | 0.5 | 0.5 | 0.5 |
Map sharpening B factor (Å2) | −187 | −158.5 | −182.1 |
Model composition | |||
Non-hydrogen atoms | 14,375 | 13,017 | 13,481 |
Protein residues | 1753 | 1586 | 1641 |
Nucleotide residues | 0 | 0 | 0 |
Ligands | 4 | 1 | 3 |
B factors (mean, Å2) | |||
Protein | 100.30 | 79.71 | 125.60 |
Nucleotide | n.a. | n.a. | n.a. |
Ligand | 125.39 | 107.78 | 124.46 |
R.m.s deviations | |||
Bond lengths (Å) | 0.003 | 0.007 | 0.017 |
Bond angles (°) | 0.662 | 1.115 | 1.652 |
Validation | |||
MolProbity score | 1.94 | 1.89 | 1.93 |
Clashscore | 7.19 | 5.54 | 6.24 |
Poor rotamers (%) | 0.19 | 0.00 | 0.14 |
Ramachandran plot | |||
Favored (%) | 90.30 | 88.37 | 88.41 |
Allowed (%) | 9.35 | 10.67 | 11.10 |
Disallowed (%) | 0.34 | 0.976 | 0.50 |
