7A4A | pdb_00007a4a

Envelope glycprotein of endogenous retrovirus Y032 (Atlas virus) from the human hookworm Ancylostoma ceylanicum

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EGU

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.086
f_angle_d	0.673
f_chiral_restr	0.043
f_bond_d	0.007
f_plane_restr	0.005

Sample
Viral envelope glycoprotein

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Grids were blotted for 4 s

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	197145
Reported Resolution (Å)	3.76
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C3

Map-Model Fitting and Refinement
Id	1 (6EGU)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value	82
Fitting Procedure
Details	A homology model was built from PDB:6EGU using the Swiss-Model server (swissmodel.expasy.org). The model was docked as a rigid body into the density with UCSF Chimera prior to refinement.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	46.18

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1300
Maximum Defocus (nm)	3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification	75000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.0
IMAGE ACQUISITION	EPU	1.9.1
CTF CORRECTION	Gctf	0.5
MODEL FITTING	UCSF Chimera	1.13.1
MODEL REFINEMENT	PHENIX	1.15rc3-3435
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.0
CLASSIFICATION	RELION	3.0
RECONSTRUCTION	RELION	3.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Aligned, non-dose-weighted micrographs were then used to estimate the CTF.	987570	2D references from initial datasets were used to auto-pick the micrographs. One round of reference-free 2D classification was performed to produce templates for better reference-dependent auto-picking.