Table 2 Cryo-EM data collection, refinement and validation statistics

From: Structural basis of tRNA recognition by the m3C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase

 

METTL6–SerRS–tRNA, 1: 2: 2

(EMD-17528), (PDB 8P7B)

METTL6–SerRS–tRNA, 2: 2: 2

(EMD-17529), (PDB 8P7C)

METTL6–SerRS–tRNA, 1: 2: 1

(EMD-17530), (PDB 8P7D)

SerRS–tRNA, 2: 1

(EMD-17531)

Free tRNA

(EMD-17532)

Data collection and processing

Magnification

130,000

130,000

130,000

130,000

130,000

Voltage (kV)

300

300

300

300

300

Electron exposure (e−/Å2)

63.27

63.27

63.27

63.27

63.27

Defocus range (μm)

−0.8 to −1.8

−0.8 to −1.8

−0.8 to −1.8

−0.8 to −1.8

−0.8 to −1.8

Pixel size (Ã…)

0.645

0.645

0.645

0.645

0.645

Symmetry imposed

C1

C2

C1

C1

C1

Initial particle images (no.)

1,625,946

1,625,946

1,625,946

1,625,946

1,625,946

Final particle images (no.)

460,853

105,928

35,788

49,372

112,675

Map resolution (Ã…)

2.4

3.7

4.2

3.8

5.6

FSC threshold

0.143

0.143

0.143

0.143

0.143

Map resolution range (Ã…)

2.2–3.4

3.0–7.0

4.0–8.0

3.3–5.7

5.0–7.0

Refinement

Initial model used (PDB code)

4RQE, 8OWX

8P7B

8P7B

  

Model resolution (Ã…)

2.4

3.7

4.2

  

FSC threshold

0.143

0.143

0.143

  

Model resolution range (Ã…)

2.2–3.4

3.0–7.0

4.0–8.0

  

Map sharpening B factor (Ã…2)

−65.1

−121.2

−101.8

  

Model composition

Nonhydrogen atoms

12,363

14,275

9,686

  

 Protein residues

1,143

1,383

1,008

  

 Ligands

1

2

1

  

B factors (Ã…2)

Protein

77.74

215.93

310.45

  

Ligand

103.19

252.95

379.51

  

R.m.s. deviations

Bond lengths (Ã…)

0.024

0.024

0.021

  

Bond angles (°)

1.767

1.755

1.557

  

Validation

MolProbity score

1.58

1.95

1.59

  

Clashscore

7.19

15.95

6.68

  

Poor rotamers (%)

0.44

1.02

0.50

  

Ramachandran plot

Favored (%)

96.89

96.40

96.58

  

Allowed (%)

3.11

3.60

3.42

  

Disallowed (%)

0.00

0.00

0.00

  
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