Table 1 Cryo-EM data collection, refinement and validation statistics. C1 cpzA3H–VCBC (EMDB-47805), (PDB 9E9V) and C2 (EMDB-47752), (PDB 9E93)

From: HIV-1 vif mediates ubiquitination of the proximal protomer in the APOBEC3H dimer to induce degradation

Data collection and processing

 Microscope

Talos Arctica

Talos Arctica

 Detection camera

Gatan K3

Gatan K3

 Voltage (kV)

200

200

 Magnification

100,000

100,000

 Electron exposure (e − / Å2)

45

45

 Defocus range (μm)

0.8 − 2.2

0.8 − 2.2

 Pixel size (Å)

0.81

0.81

 Symmetry imposed

C2

C1

 Initial particle images (no.)

10,231,372

6,580,020

 Final particle images (no.)

201,593

215,818

 Map resolution (Å)

3.63

4.0

 FSC threshold

0.143

0.143

 Map resolution range (Å)

2.97-8.0

3.5-7.7

Model building and refinement

 Initial model used (PDB code)

4N9F, 5Z98

4N9F, 5Z98

 Model resolution (Å)

4.0

4.55

 FSC threshold

0.5

0.5

 Model resolution range (Å)

3.0-6.0

3.4-6.6

 Map sharpening B factor (Å)a

-135.9

-143.6

 B factors (Å2)

  

  Protein

83.51

160.61

  Nucleotide

84.91

107.42

  Ligand

102.2

182.24

R.m.s. deviations

 Bond lengths (Å)

0.002

0.001

 (outliers >4 sigma)

0

0

 Bond angles (°)

0.397

0.405

 (outliers >4 sigma)

2

6

Validation

 MolProbity score

1.29

1.34

 Clashscore

5.46

4.31

 Rotamer outliers (%)

0.0

0

 CaBLAM outliers (%)

1.3

1.19

 Cβ outliers (%)

0

0

Ramachandran plot

 Favored (%)

98.52

97.35

 Allowed (%)

1.48

2.65

 Outliers (%)

0.0

0.0

Model composition

 Nonhydrogen atoms

8,773

10,936

 Protein residues

965

1241

 Nucleotide residues

32

32

 Ligands

ZN: 4

ZN: 4

Real-space correlation

 CCvolume

0.75

0.6

 CCmask

0.75

0.61