Table 1 Cryo-ET data collection and structure refinement statistics of high-resolution ribosome averages in Cm-treated cells

From: Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells

 

70S ribosome average

(EMD-17132), (PDB 8P7X)

30S SSU

(EMD-17133), (PDB 8P6P)

50S LSU

(EMD-17134), (PDB 8P8B)

70S with S4LSU

(EMD-17135), (PDB 8P7Y)

Data collection and processing

Magnification

64,000

Voltage (kV)

300

Electron exposure (e− per Å2)

137

Electron exposure per tilt image (e− per Å2)

3.34

Energy filter slit width (eV)

20

Tilt range and scheme

−60°:3°:60°; dose symmetric

Defocus range (μm)

−1.0 to −3.25

Pixel size (Å)

1.329

Symmetry imposed

C1

Initial subtomograms (no.)

30,774

30,774

30,774

30,774

Final subtomograms (no.)

30,774

30,774

30,774

10,151

Map resolution (Å)

 FSC threshold = 0.143

3.0

3.2

2.9

3.7

Map resolution range (Å)

2.8 to 6

3 to 5

2.8 to 4

3.2 to 6

Map sharpening B factor (Å2)

−1 to +15

−1 to +15

−1 to +15

−1 to +15

Model refinement

Initial model used (PDB code)

7OOC, 7OOD

7OOC

7OOD

7OOC, 7OOD

Model resolution (Å)

 FSC threshold = 0.143

3.02

3.28

3.08

3.62

Model resolution (Å)

 FSC threshold = 0.5

3.28

3.60

3.16

4.04

Model versus map correlation coefficient

0.73

0.74

0.80

0.73

Model composition

 Nonhydrogen atoms

151,587

55,468

97,171

153,258

 Protein residues

6,182

2,597

3,578

6,386

 RNA residues

4,755

1,612

3,194

4,755

 Ligands and water

367

112

266

369

B factors (Å2) (mean)

 Protein

70.84

82.90

62.04

71.55

 RNA

73.77

88.29

67.03

73.77

 Ligands

31.27

29.99

31.44

31.27

 Water

-

30.00

-

-

R.m.s.d.

 Bond lengths (Å)

0.003

0.003

0.004

0.005

 Bond angles (°)

0.580

0.555

0.592

0.750

Validation

 MolProbity score

1.93

2.03

2.20

2.10

 Clashscore

8.98

10.60

7.63

13.04

 Poor rotamers (%)

0.83

0.58

3.75

1.00

Ramachandran plot

 Favored (%)

92.84

91.85

95.02

92.23

 Allowed (%)

6.71

7.72

4.89

7.14

 Disallowed (%)

0.44

0.43

0.09

0.64

Validation (RNA)

    

 Good sugar pucker (%)

99.20

99.50

99.53

99.26

 Good backbone (%)

81.42

84.40

81.70

81.49

Back to article page