Table 2 Cryo-ET data processing and structure refinement statistics of 70S ribosome and disome classes in Cm-treated cells
From: Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells
70S class ‘A, P’ | 70S class ‘A, P, E’ | 70S class ‘a, P’ | 70S class ‘a, P, E’ | 70S class ‘EF-Tu•tRNA, P’ | 70S class ‘EF-Tu•tRNA, P, E’ | 70S class ‘A*, P/E’ | Disome class I | Disome class II | Disome class III | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
PDB 8P8V (leading ribosome) | PDB 8P8W (following ribosome) | ||||||||||
EMD-17136 | EMD-17137 | EMD-17138 | EMD-17139 | EMD-17140 | EMD-17141 | EMD-17142 | EMD-17143 | EMD-17144 | EMD-17145 | ||
Data collection and processinga | |||||||||||
Final subtomogram (no.) | 8,854 | 6,478 | 2,713 | 2,948 | 3,977 | 3,071 | 787 | 654 | 387 | 963 | |
Map resolution (Å) | |||||||||||
FSC threshold = 0.143 | 3.6 | 3.8 | 4.4 | 4.4 | 4.4 | 4.4 | 7.6 | 10 | 15 | 8.7 | |
Map resolution range (Å) | 3.2 to 4.2 | 3.4 to 4.5 | 4 to 6 | 4 to 6 | 4 to 8 | 4 to 8 | 6 to 10 | 6 to 25 | 8 to 25 | 5 to 15 | |
B factor (Å2) | −7 | −5 | −8 | −8 | −1 | −5 | −22 | −100 | −150 | −50 | |
Model refinement | |||||||||||
Initial model used (PDB code) | |||||||||||
Model resolution (Å) | |||||||||||
FSC threshold = 0.143 | 8.52 | 8.63 | |||||||||
Model resolution (Å) | |||||||||||
FSC threshold = 0.5 | 8.92 | 11.10 | |||||||||
Model versus map correlation coefficient | 0.76 | 0.60 | |||||||||
Model composition | |||||||||||
Nonhydrogen atoms | 153,639 | 151,556 | |||||||||
Protein residues | 6,436 | 6,394 | |||||||||
RNA residues | 4,773 | 4,688 | |||||||||
Ligands | 334 | 316 | |||||||||
B factors (Å2) (mean) | |||||||||||
Protein | 71.46 | 71.48 | |||||||||
RNA | 76.15 | 77.10 | |||||||||
Ligand | 35.81 | 38.68 | |||||||||
R.m.s.d. | |||||||||||
Bond lengths (Å) | 0.004 | 0.003 | |||||||||
Bond angles (°) | 0.721 | 0.638 | |||||||||
Validation | |||||||||||
MolProbity score | 2.20 | 2.17 | |||||||||
Clashscore | 16.58 | 14.33 | |||||||||
Poor rotamers (%) | 0.07 | 0.00 | |||||||||
Ramachandran plot | |||||||||||
Favored (%) | 92.18 | 91.42 | |||||||||
Allowed (%) | 7.02 | 7.64 | |||||||||
Disallowed (%) | 0.81 | 0.94 | |||||||||
Validation (RNA) | |||||||||||
Good sugar pucker (%) | 99.22 | 99.25 | |||||||||
Good backbone (%) | 81.14 | 81.24 | |||||||||
