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

From: Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels

Structure

GluK2NpTx8

GluK2PhTx74

GluK2KukoA

GluK2SPM

EMDB accession code

EMD-47296

EMD-47295

EMD-47298

EMD-47297

PDB accession code

9DXR

9DXQ

9DXT

9DXS

Data collection and processing

 Voltage (kV)

300

300

300

300

 Electron exposure (e−Å−2)

50

40

47.25

54.4

 Reported pixel size (Å)

1.055

0.832

1.069

0.835

 Processing software

CryoSPARC v4

CryoSPARC v4

CryoSPARC v4

CryoSPARC v4

 Symmetry imposed

C2

C2

C2

C2

 Final particle images (no.)

199,303

238,611

211,509

193,200

 Map resolution (Å)

3.10

2.81

3.75

3.55

 FSC threshold

0.143

0.143

0.143

0.43

Refinement

 Initial models used (PDB code)

8FWS

8FWS

8FWS

8FWS

 Model resolution (Å)

3.10

2.81

3.75

3.55

 Mask CC

0.79

0.83

0.78

0.84

 Volume CC

0.72

0.81

0.78

0.83

 Map sharpening B factor (Å2)

−107.1

−133.4

−150.8

−146.5

B factors (Å2)

 Protein

102.77

99.39

123.85

129.08

 Ligands

79.77

77.55

127.62

140.84

R.m.s. deviations

 Bond lengths (Å)

0.010

0.011

0.010

0.010

 Bond angles (°)

1.477

1.423

1.494

1.418

Model composition

 Non-hydrogen atoms

15333

15555

15138

15294

 Protein residues

1784

1784

1784

1784

Ligands

 2J9 (BPAM344)

4

4

4

4

 BMA

4

4

4

4

 NAG

16

16

16

14

 POV

16

16

8

12

 CL

–

2

–

–

 NA

–

6

–

–

 CLR

–

8

8

8

 Channel blocker

1 (NTX)

1 (PTX)

1 (KUK)

1 (SPM)

Validation

 MolProbity score

1.87

1.75

1.97

1.83

 Clash score, all atoms

4.67

4.14

4.54

4.38

 Outliers rotamers (%)

1.16

1.03

0.26

0.90

Ramachandran plot

 Favored (%)

88.66

90.29

79.28

87.50

 Allowed (%)

10.78

9.37

17.57

11.60

 Outliers (%)

0.56

0.34

3.14

0.90

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