Table 1 Cryo-EM refinement parameters and model validation
From: Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis
CHI (EMDB-51350) (PDB 9GHA) | POST (EMDB-51351) (PDB 9GHB) | FusB•EF-G•70S (EMDB-51352) (PDB 9GHC) | FusB•EF-G•70S* (EMDB-51353) (PDB 9GHD) | FusB•70S:SSU (EMDB-51354) (PDB 9GHE) | FusB•70S:LSU (EMDB-51355) (PDB 9GHF) | FusB•Sa70S:SSU (EMDB-51356) (PDB 9GHG) | FusB•Sa70S:LSU (EMDB-51357) (PDB 9GHH) | |
|---|---|---|---|---|---|---|---|---|
Data collection and processing | ||||||||
Dataset | Early | Early | Early | 25 s | 25 s | 25 s | FusB•Sa70S | FusB•Sa70S |
Magnification | 130,000 | 130,000 | 130,000 | 130,000 | 130,000 | 130,000 | 165,000 | 165,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e–/Å2) | 40 | 40 | 40 | 45.47 | 45.47 | 45.47 | 28.14 | 28.14 |
Defocus range (μm) | −0.7 to −1.0 | −0.7 to −1.0 | −0.7 to −1.0 | −0.7 to −1.0 | −0.7 to −1.0 | −0.7 to −1.0 | −0.7 to −1.0 | −0.7 to −1.0 |
Pixel size (Å) | 0.6480 | 0.6480 | 0.6480 | 0.6478 | 0.6478 | 0.6478 | 0.7280 | 0.7280 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particle images (no.) | 2,239,537 | 2,239,537 | 2,239,537 | 3,613,403 | 3,613,403 | 3,613,403 | 859,410 | 859,410 |
Final particle images (no.) | 88,568 | 184,659 | 34,617 | 30,847 | 349,231 | 29,766 | 67,441 | 15,167 |
Map resolution (Å) | 2.24 | 2.21 | 2.79 | 2.41 | 1.87 | 2.40 | 2.22 | 2.70 |
FSC threshold | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 | 0.143 |
Refinement | ||||||||
Initial model used (PDB code) | 9GHE | 9GHE | 9GHE | 9GHE | 8CGK, 8CGJ, 8CF1, 7K00, 7N2C, 4ADN | 9GHE | 8P2F, 4ADN | 9GHG |
Model resolution (Å) | 2.2 | 2.2 | 2.8 | 2.4 | 1.9 | 2.4 | 2.2 | 2.7 |
FSC threshold | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
Post-processing | Local filtering | Local filtering | Local filtering | Local filtering | Local filtering | Local filtering | Local filtering | Local filtering |
Map sharpening B factor. (Å2) | −35 | −36 | −25 | −33 | −36 | −33 | −32 | −23 |
Model composition | ||||||||
Non-hydrogen atoms | 145,564 | 145,490 | 147,172 | 143,666 | 146,257 | 141,978 | 150,404 | 144,758 |
Protein residues | 6176 | 6188 | 6380 | 5946 | 5718 | 5718 | 5685 | 5680 |
RNA residues | 4510 | 4499 | 4502 | 4498 | 4501 | 4501 | 4654 | 4650 |
Waters | 0 | 0 | 0 | 0 | 4235 | 0 | 5514 | 0 |
Magnesium atoms | 272 | 303 | 301 | 303 | 303 | 303 | 145 | 145 |
B factors (Å2) | ||||||||
Protein | 72 | 71 | 81 | 69 | 57 | 62 | 72 | 91 |
RNA | 57 | 54 | 62 | 51 | 45 | 50 | 65 | 79 |
Ligand | 41 | 44 | 49 | 39 | 30 | 38 | 30 | 44 |
Water | – | – | – | – | 24 | – | 38 | – |
R.m.s. deviations | ||||||||
Bond lengths (Å) | 0.008 | 0.008 | 0.008 | 0.008 | 0.008 | 0.008 | 0.008 | 0.008 |
Bond angles (°) | 1.187 | 1.183 | 1.175 | 1.191 | 1.294 | 1.195 | 1.193 | 1.198 |
Validation | ||||||||
MolProbity score | 1.30 | 1.12 | 1.22 | 1.06 | 1.04 | 1.12 | 1.38 | 1.38 |
Clashscore | 3.47 | 2.87 | 3.60 | 2.5 | 2.54 | 3.02 | 4.17 | 3.49 |
Poor rotamers (%) | 1.24 | 0.83 | 1.23 | 1.08 | 0.95 | 1.10 | 1.73 | 1.69 |
Ramachandran plot | ||||||||
Favored (%) | 97.57 | 97.79 | 98.50 | 98.66 | 98.52 | 98.68 | 98.67 | 98.78 |
Allowed (%) | 2.31 | 2.08 | 1.44 | 1.29 | 1.45 | 1.29 | 1.31 | 1.20 |
Disallowed (%) | 0.12 | 0.13 | 0.06 | 0.05 | 0.04 | 0.04 | 0.02 | 0.02 |
Rama-Z score | −0.54 | −0.54 | 1.19 | 0.88 | 1.13 | 1.23 | 1.07 | 0.99 |
