6DFF | pdb_00006dff

Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4P6Z
experimental model	PDB	4HMY
experimental model	PDB	1O3Y

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.405
f_angle_d	0.825
f_chiral_restr	0.053
f_plane_restr	0.006
f_bond_d	0.005

Sample
AP-1:Arf1:tetherin-Nef
Sample Components
AP-1 sigma-3:Arf1:tetherin-Nef
AP-1 mu-1 and gamma-1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	53123
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4P6Z, 4HMY, 1O3Y)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Correlation coefficient
Overall B Value
Fitting Procedure
Details	Phenix real space refine

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	62.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	750
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.6
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	22500
Calibrated Magnification	46849
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Gautomatch	0.5
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	1.12
INITIAL EULER ASSIGNMENT	RELION
FINAL EULER ASSIGNMENT	RELION	2.1
CLASSIFICATION	RELION	2.1
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.13

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		252212

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.