Table 1.
Cryo-EM data collection, refinement and validation statistics.
| SPT (EMD-22598, PDB 7K0I) |
SPT (protomer) (EMD-22599, PDB 7K0J) |
SPT-3KS (protomer) (EMD-22600, PDB 7K0K) |
SPT-myriocin (protomer) (EMD-22601, PDB 7K0L) |
SPT-ORM (class 1) (EMD-22602, PDB 7K0M) |
SPT-ORM (class 2) (EMD-22604, PDB 7K0N) |
SPT-ORM (class 3) (EMD-22605, PDB 7K0O) |
SPT-ORM (class 4) (EMD-22606, PDB 7K0P) |
SPT-ORM-myriocin (protomer) (EMD-22608, PDB 7K0Q) |
|
|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||
| Data collection and processing | |||||||||
| Magnification | 63,000 | 63,000 | 81,000 | 63,000 | 63,000 | 63,000 | 63,000 | 63,000 | 63,000 |
| Voltage (kV) | 200 | 200 | 300 | 200 | 200 | 200 | 200 | 200 | 200 |
| Electron exposure (e−/Å2) | 60.35 | 60.35 | 80.50 | 70.67 | 72.53 | 72.53 | 72.53 | 72.53 | 70.67 |
| Defocus range (μm) | 1–2 | 1–2 | 1–2 | 1–2 | 1–2 | 1–2 | 1–2 | 1–2 | 1–2 |
| Pixel size (Å) | 1.00 | 1.00 | 1.06 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| Symmetry imposed | C2 | C1 | C1 | C1 | C2 | C2 | C2 | C1 | C1 |
| Initial particle images (no.) | ~1,200,000 | ~1,200,000 | ~4,900,000 | ~3,900,000 | ~4,200,000 | ~4,200,000 | ~4,200,000 | ~4,200,000 | ~3,900,000 |
| Final particle images (no.) | 238,610 | 157,895 | 133,308 | 118,539 | 169,428 | 195,572 | 221,541 | 198,543 | 191,726 |
| Map resolution (Å) | 3.3 | 3.1 | 2.6 | 3.4 | 2.9 | 3.1 | 3.1 | 3.1 | 3.3 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Map resolution range (Å) | 3.3–200 | 3.1–200 | 2.6–200 | 3.4–200 | 2.9–200 | 3.1–200 | 3.1–200 | 3.1–200 | 3.3–200 |
| Refinement | |||||||||
| Initial model used (PDB code) | de novo | de novo | de novo | de novo | de novo | de novo | de novo | de novo | de novo |
| Model resolution (Å) | 3.3 | 3.1 | 2.6 | 3.4 | 2.9 | 3.1 | 3.1 | 3.1 | 3.3 |
| FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
| Model resolution range (Å) | 3.3–200 | 3.1–200 | 2.6–200 | 3.4–200 | 2.9–200 | 3.1–200 | 3.1–200 | 3.1–200 | 3.3–200 |
| Map sharpening B factor (Å2) | −96.3 | −75.4 | −39.0 | −81.3 | −86.2 | −88.9 | −87.7 | −82.3 | −56.6 |
| Model composition | |||||||||
| Nonhydrogen atoms | 15,366 | 7,683 | 7,615 | 7,619 | 18,578 | 18,470 | 18,558 | 18,572 | 8,778 |
| Protein residues | 1,954 | 977 | 964 | 964 | 2,342 | 2,340 | 2,342 | 2,342 | 1,107 |
| Ligands | 6 | 3 | 2 | 2 | 16 | 18 | 14 | 15 | 2 |
| B factors (Å2) | |||||||||
| Protein | 43.36 | 79.69 | 50.34 | 63.13 | 83.66 | 37.62 | 54.71 | 64.06 | 73.58 |
| Ligand | 44.31 | 91.90 | 50.38 | 66.84 | 88.59 | 33.77 | 54.70 | 66.12 | 74.48 |
| R.m.s. deviations | |||||||||
| Bond lengths (Å) | 0.005 | 0.006 | 0.006 | 0.004 | 0.003 | 0.003 | 0.005 | 0.004 | 0.006 |
| Bond angles (°) | 0.617 | 0.688 | 0.656 | 0.575 | 0.524 | 0.572 | 0.647 | 0.610 | 0.678 |
| Validation | |||||||||
| MolProbity score | 1.62 | 1.49 | 1.45 | 1.21 | 1.30 | 1.44 | 1.44 | 1.37 | 1.48 |
| Clashscore | 6.19 | 5.48 | 7.43 | 4.27 | 4.67 | 6.22 | 5.84 | 5.21 | 5.12 |
| Poor rotamers (%) | 0.25 | 0 | 0 | 0 | 0 | 0.32 | 0 | 0 | 0 |
| Ramachandran plot | |||||||||
| Favored (%) | 95.98 | 96.81 | 97.81 | 98.12 | 97.72 | 97.5 | 97.38 | 97.55 | 96.72 |
| Allowed (%) | 4.02 | 3.19 | 2.79 | 1.88 | 2.28 | 2.5 | 2.62 | 2.45 | 3.28 |
| Disallowed (%) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |