Table 1 Cryo-EM data collection, refinement and validation statistics

From: Structural insight into the intraflagellar transport complex IFT-A and its assembly in the anterograde IFT train

 

IFT-A_ Elongated (EMD-34893)

IFT-A_ Folded (EMD-34894)

IFT-A_ Base-1 (EMD-34895) (PDB 8HMC)

IFT-A_ Base-2 (EMD-34896) (PDB 8HMD)

IFT-A_ Head-1 (EMD-34897) (PDB 8HME)

IFT-A_ Head-2 (EMD-34898) (PDB 8HMF)

IFT-A_ Head-3 (EMD-34899)

Data collection and processing

Magnification

×81,000

×81,000

×81,000

×81,000

×81,000

×81,000

×81,000

Voltage (kV)

300

300

300

300

300

300

300

Electron exposure (e–/Å2)

50.0

50.0

50.0

50.0

50.0

50.0

50.0

Defocus range (μm)

1.5–2.5

1.5–2.5

1.5–2.5

1.5–2.5

1.5–2.5

1.5–2.5

1.5–2.5

Pixel size (Å)

1.10

1.10

1.10

1.10

1.10

1.10

1.10

Symmetry imposed

C1

C1

C1

C1

C1

C1

C1

Initial particle images (no.)

1,225,162

101,666

1,239,500

1,239,500

1,225,162

1,225,162

1,225,162

Final particle images (no.)

35,628

14,020

538,078

86,362

386,801

199,946

41,877

Map resolution (Å)

8.5

8.8

3.6

4.7

4.2

4.6

6.0

FSC threshold

0.143

0.143

0.143

0.143

0.143

0.143

0.143

Map resolution range (Å)

7.0–14.0

7.0–12.0

3.2–5.0

4.0–8.0

4.0–6.0

4.0–8.0

5.5–10.0

Refinement

Initial model used (PDB code)

  

n/a

n/a

n/a

n/a

 

Model resolution (Å)

  

n/a

n/a

n/a

n/a

 

FSC threshold

  

n/a

n/a

n/a

n/a

 

Model resolution range (Å)

  

n/a

n/a

n/a

n/a

 

Map sharpening B factor (Å2)

  

−106

−120

−126

−152

 

Model composition

       

   Non-hydrogen atoms

  

21,797

27,372

22,169

25,330

 

   Protein residues

  

2693

3387

2745

3135

 

   Ligands

  

2

2

2

2

 

B factors (Å2)

   Protein

  

72.06

117.41

78.33

86.15

 

   Ligand

  

174.17

336.87

116.42

127.01

 

R.m.s. deviations

       

   Bond lengths (Å)

  

0.011

0.003

0.002

0.002

 

   Bond angles (°)

  

1.060

0.619

0.587

0.599

 

Validation

   MolProbity score

  

1.87

1.88

1.93

1.87

 

   Clashscore

  

8.57

9.86

11.78

11.53

 

   Poor rotamers (%)

  

0.13

0.03

0.00

0.04

 

   Ramachandran plot

       

   Favored (%)

  

93.97

944.70

95.11

95.78

 

   Allowed (%)

  

6.00

5.24

4.71

4.03

 

   Disallowed (%)

  

0.04

0.06

0.18

0.19

 
Back to article page