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

From: Proton-triggered rearrangement of the AMPA receptor N-terminal domains impacts receptor kinetics and synaptic localization

GluA2flip(Q)–TARPγ2

pH 8 consensus LBD–TMD–STG; EMD-44232, PDB 9B5Z

pH 8 consensus TMD–STG; EMD-44233, PDB 9B60

pH 8 class 1 LBD–TMD–STG; EMD-44248, PDB 9B67

pH 8 class 1 NTD; EMD-44249, PDB 9B68

Data collection and processing

Microscope

Titan Krios G4

Titan Krios G4

Titan Krios G4

Titan Krios G4

Detector

BioQuantumK3

BioQuantumK3

BioQuantumK3

BioQuantumK3

Magnification

×105,000

×105,000

×105,000

×105,000

Voltage (kV)

300

300

300

300

Electron exposure (e− per Å2)

52.8

52.8

52.8

52.8

Defocus range (μm)

−1.0 to −2.4

−1.0 to −2.4

−1.0 to −2.4

−1.0 to −2.4

Pixel size (Ã…)

0.820

0.820

0.820

0.820

Symmetry imposed

C1

C1

C1

C1

No. of micrographs

21,898

21,898

21,898

21,898

Final particle images (no.)

1,108,462

1,108,462

47,782

47,782

Map resolution (Ã…)

2.71

2.57

3.39

3.60

 FSC threshold

0.143

0.143

0.143

0.143

Map resolution range (Ã…)

2.49–4.33

2.43–4.40

3.03–6.33

3.49–6.61

Refinement

Initial model used (PDB code)

8FPG, 8FPK

8FPG, 8FPK

8FPG, 8FPK

6U6I

Model resolution (Ã…)

2.2/2.8

2.3/2.7

2.7/3.4

3.3/3.6

 FSC threshold

0.5/0.143

0.5/0.143

0.5/0.143

0.5/0.143

Map sharpening B factor (Ã…2)

−77.8 (−30)a

−72.3

−87

−79.9

Model composition

 Nonhydrogen atoms

18,684

10,461

18,439

11,364

 Protein residues

2,406

1,348

2,372

1,496

 Ligands

   

BMA: 2

    

NAG: 9

B factors (Ã…2)

 Protein

86.44

49.87

39.29

41.11

 Ligand

   

64.49

R.m.s.d.

 Bond lengths (Å)

0.003

0.002

0.003

0.003

 Bond angles (°)

0.559

0.447

0.481

0.575

Validation

 MolProbity score

1.80

1.55

1.42

1.55

 Clashscore

7.97

4.52

6.28

6.35

 Poor rotamers (%)

2.08

1.57

0.26

0.27

Ramachandran plot

 Favored (%)

97.33

97.00

97.67

97.11

 Allowed (%)

2.62

3.00

2.33

2.89

 Disallowed (%)

0.04

0.00

0.00

0.00

GluA2flip(Q)–TARPγ2

pH 8 class 12 LBD–TMD–STG; EMD-44251, PDB 9B6A

pH 8 class 12 NTD; EMD-44250, PDB 9B69

pH 5.5 consensus LBD–TMD–STG; EMD-44234, PDB 9B61

pH 5.5 consensus TMD–STG; EMD-44244, PDB 9B63

Data collection and processing

Microscope

Titan Krios G4

Titan Krios G4

Titan Krios G4

Titan Krios G4

Detector

BioQuantumK3

BioQuantumK3

BioQuantumK3

BioQuantumK3

Magnification

×105,000

×105,000

×105,000

×105,000

Voltage (kV)

300

300

300

300

Electron exposure (e− per Å2)

52.8

52.8

55.6

55.6

Defocus range (μm)

−1.0 to −2.4

−1.0 to −2.4

−1.0 to −2.4

−1.0 to −2.4

Pixel size (Ã…)

0.820

0.820

0.820

0.820

Symmetry imposed

C1

C1

C1

C1

No. of micrographs

21,898

21,898

19,684

19,684

Final particle images (no.)

48,399

48,399

813,615

813,615

Map resolution (Ã…)

3.35

3.69

2.81

2.76

 FSC threshold

0.143

0.143

0.143

0.143

Map resolution range (Ã…)

3.04–6.55

3.42–6.92

2.66–6.06

2.65–4.63

Refinement

Initial model used (PDB code)

8FPG, 8FPK

8FPG, 8FPK

8FPG, 8FPK

8FPG, 8FPK

Model resolution (Ã…)

2.7/3.4

3.1/3.6

2.6/3.0

2.5/2.8

 FSC threshold

0.5/0.143

0.5/0.143

0.5/0.143

0.5/0.143

Map sharpening B factor (Ã…2)

−91.6

−97.4

−84.6 (−30)a

−83.7

Model composition

 Nonhydrogen atoms

18,497

11,370

18,415

10,461

 Protein residues

2,378

1,496

2,384

1,348

 Ligands

 

BMA: 2

  
  

NAG: 9

  

B factors (Ã…2)

 Protein

32.63

62.33

119.67

48.25

 Ligand

 

91.91

  

R.m.s.d.

 Bond lengths (Å)

0.003

0.002

0.005

0.002

 Bond angles (°)

0.495

0.449

0.800

0.475

Validation

 MolProbity score

1.43

1.47

2.05

1.73

 Clashscore

7.42

5.52

10.98

4.77

 Poor rotamers (%)

0.21

0.27

3.00

2.22

Ramachandran plot

 Favored (%)

97.89

97.04

97.34

96.54

 Allowed (%)

2.11

2.96

2.66

3.46

 Disallowed (%)

0.00

0.00

0.00

0.00

GluA2flip(Q)–TARPγ2

pH 5.5 class 23 LBD–TMD–STG; EMD-44245, PDB 9B64

pH 5.5 class 23 NTD; EMD-44245c

Data collection and processing

Microscope

Titan Krios G4

Titan Krios G4

Detector

BioQuantumK3

BioQuantumK3

Magnification

×105,000

×105,000

Voltage (kV)

300

300

Electron exposure (e– per Å2)

55.6

55.6

Defocus range (μm)

−1.0 to −2.4

−1.0 to −2.4

Pixel size (Ã…)

0.820

0.820

Symmetry imposed

C1

C1

No. of micrographs

19,684

19,684

Final particle images (no.)

29,945

29,945

Map resolution (Ã…)

3.56

5.90

 FSC threshold

0.143

0.143

Map resolution range (Ã…)

3.27–7.57

5.90–9.04

Refinement

Initial model used (PDB code)

8FPG, 8FPK

6U6I

Model resolution (Ã…)

3.1/3.6

ND

 FSC threshold

0.5/0.143

 

Map sharpening B factor (Ã…2)

−90.6

−214 (−80)b

Model composition

 Nonhydrogen atoms

18,497

ND

 Protein residues

2,378

ND

 Ligands

  

B factors (Ã…2)

 Protein

97.32

ND

 Ligand

  

R.m.s.d.

 Bond lengths (Å)

0.003

ND

 Bond angles (°)

0.639

ND

Validation

 MolProbity score

1.63

ND

 Clashscore

9.56

ND

 Poor rotamers (%)

0.21

ND

Ramachandran plot

 Favored (%)

97.38

ND

 Allowed (%)

2.62

ND

 Disallowed (%)

0.00

ND

  1. Map sharpening B factors were determined by RELION postprocessing, unless otherwise noted. BMA, β-d-mannopyranose; NAG, 2-acetamido-2-deoxy-β-d-glucopyranose; ND, not determined because of low-resolution map.
  2. aA B factor of −30 was used to refine the atomic model (the B factor outside the parentheses was determined by RELION).
  3. bA B factor of −80 was used to interpret the map (a B factor of −214 was determined by RELION).
  4. cDeposited as an associated map.
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