Table 1 Statistics of cryo-EM data collection, refinement and validation

From: Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε

 

Pol ε–PCNA on matched DNA, no detergent

Pol ε–PCNA on matched DNA, 8 mM CHAPSO

Pol ε–PCNA on mismatched DNA, no detergent

Pol ε–PCNA on mismatched DNA, 8 mM CHAPSO

Data collection

Microscope

FEI Titan Krios

FEI Titan Krios

FEI Titan Krios

FEI Titan Krios

Voltage (kV)

300

300

300

300

Camera

Gatan K3

Falcon 4i

Gatan K3

Gatan K3

Magnification

×105,000

×96,000

×105,000

×105,000

Electron exposure (e− per Å2)

40.08

40.18

36.4

39.9

Defocus range (μm)

−0.8 to −3.0

−0.8 to −3.0

−1.2 to −3.0

−1.2 to −3.0

Pixel size (Å)

0.73

0.824

0.73

0.73

Micrographs collected

13,522

12,784

9,659

13,159

Total extracted particles (no.)

2.61 million

3.89 million

3.88 million

3.52 million

Reconstruction

Pol ε–PCNA, Open conf.

Pol ε–PCNA, Ajar conf.

Pol ε–PCNA, Closed conf.

Proofreading Post-Insertion

Proofreading Pol Arrest

Proofreading Frayed Substrate

Proofreading Mismatch Excision

EM Data Bank

EMD-50222

EMD-50223

EMD-50224

EMD-50225

EMD-50226

EMD-50227

EMD-50228

PDB

9F6D

9F6E

9F6F

9F6I

9F6J

9F6K

9F6L

Symmetry imposed

None

None

None

None

None

None

None

Final particle images (no.)

175,614

69,268

92,356

119,518

44,918

43,921

18,858

Map resolutiona (Å) 0.143 FSC threshold

3.6 (3.4)

3.7 (3.7)

3.8 (3.7)

3.3

3.9

4.2

3.9

Map resolution range (Å) 0.5 FSC threshold

3.0–5.8

3.2–6.2

3.2–6.1

3.3–5.3

3.3–9.2

3.4–9.5

3.4–11

Map sharpening B factora (Å2)

−127.2 (−109.7)

−110.3 (−98.2)

−119.3 (−105.8)

−122.1

−115

−140

−93

Model refinement

Initial model used (PDB code)

4M8O1AXC

4M8O1AXC

4M8O1AXC

4M8O

4M8O6WJV

4M8O6WJV

4M8O1CLQ

Model resolution (Å) 0.5 FSC threshold

3.8

4.1

4.1

3.5

4

4.3

4.1

Model composition nonhydrogen atoms

16,377

16,376

16,376

9,781

9,751

9,637

9,639

Protein residues

1,918

1,918

1,918

1,118

1,118

1,118

1,118

Nucleotide

52

52

52

32

32

26

26

Ligands

1 DDS, 1 SF4, 1 MG

1 DDS, 1 SF4

1 DDS, 1 SF4

1 DDS, 1 SF4, 1 CA

1 SF4

1 SF4

1 SF4, 2 CA

B factors (Å2)

Protein

40.34

91.16

98.82

27.13

86.58

125.9

111.17

 Nucleotide

108.8

155.18

160.44

65.53

149.8

198.21

162.04

 Ligand

26.52

70.08

79.11

23.21

50.08

125.48

100

R.m.s.d.

Bond lengths (Å)

0.003

0.003

0.004

0.003

0.003

0.003

0.003

Bond angles (°)

0.691

0.666

0.742

0.686

0.641

0.656

0.666

Validation

MolProbity score

0.88

0.87

1.05

0.84

0.94

1.01

0.89

Clashscore

1.46

1.4

2.67

1.2

1.83

2.22

1.48

Poor rotamers (%)

0

0

0

0

0

0.1

0

Ramachandran plot

Favored (%)

99.32

99.06

99.27

98.92

98.92

97.94

98.11

Allowed (%)

0.68

0.94

0.73

1.08

1.08

2.06

1.89

Disallowed (%)

0

0

0

0

0

0

0

  1. aStatistics for local refinements with mask around Pol ε cat are given in parentheses. DDS, ddATP; SF4, iron–sulfur cluster; CA, Ca2+; MG, Mg2+.
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