Table 1 Cryo-EM data collection, refinement and validation statistics
From: Structural insights into translocation and tailored synthesis of hyaluronan
Data collection and processing | ||||||
Magnification | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 | 81,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e− per Å2) | 50 | 50 | 50 | 50 | 50 | 50 |
Defocus range (μm) | −2.0 to −1.0 | −2.0 to −1.0 | −2.0 to −1.0 | −2.0 to −1.0 | −2.0 to −1.0 | −2.0 to −1.0 |
Pixel size (Å) | 1.08 | 1.08 | 1.08 | 1.08 | 1.08 | 1.08 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 6,543,217 | 22,061,285 | 26,290,833 | 7,978,429 | 3,663,447 | 12,554,677 |
Final particle images (no.) | 337,022 | 169,894 | 136,942 | 176,543 | 56,954 | 220,556 |
Map resolution (Å) | 3.2 | 3.0 | 3.2 | 3.2 | 3.3 | 3.0 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 2.7–6.0 | 2.6–3.5 | 2.8–5.0 | 2.4–3.5 | 2.9–4.5 | 2.3–3.4 |
Refinement | ||||||
Initial model used (PDB code) | AF2 B1WB39 | |||||
Model resolution (Å) | 3.2 | 3.0 | 3.2 | 3.2 | 3.3 | 3.0 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Map sharpening B factor (Å2) | 95.4 | 102.0 | 87.0 | 133.0 | 117.7 | 108.6 |
Model composition | ||||||
Nonhydrogen atoms | 5,930 | 6,138 | 6,097 | 6,090 | 5,928 | 6,025 |
Protein residues | 738 | 749 | 757 | 742 | 728 | 735 |
Ligands | 0 | 9 | 2 | 6 | 6 | 6 |
B factors (Å2) | ||||||
Protein | 75.6 | 35.98 | 73.11 | 68.63 | 58.44 | 52.18 |
Ligand | - | 50.07 | 60.99 | 82.53 | 54.72 | 55.03 |
R.m.s.d. | ||||||
Bond lengths (Å) | 0.004 | 0.002 | 0.002 | 0.005 | 0.004 | 0.008 |
Bond angles (°) | 0.660 | 0.519 | 0.526 | 0.985 | 0.859 | 1.054 |
Validation | ||||||
MolProbity score | 1.63 | 1.48 | 1.64 | 1.20 | 1.58 | 1.54 |
Clashscore | 6.97 | 4.61 | 6.29 | 4.23 | 5.36 | 4.92 |
Poor rotamers (%) | 0.31 | 0.15 | 0.3 | 0.0 | 0.32 | 0.16 |
Ramachandran plot | ||||||
Favored (%) | 96.28 | 96.35 | 95.72 | 98.22 | 95.81 | 95.86 |
Allowed (%) | 3.72 | 3.65 | 4.15 | 1.64 | 4.19 | 4.00 |
Disallowed (%) | 0.00 | 0.00 | 0.13 | 0.14 | 0.00 | 0.14 |
