6YGH | pdb_00006ygh

Duck hepatitis B virus capsid

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.94
f_angle_d	0.562
f_chiral_restr	0.038
f_bond_d	0.004
f_plane_restr	0.003

Sample
Hepatitis B virus duck/DHBV-16

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	For the vitrification, grids (400 mesh copper grids (type R 1.2/1.3. Quantifoil Micro Tools, Jena/Germany) were rendered hydrophilic by glow discharging in air at a pressure of 29 Pa for 2 minutes at medium power with a Plasma Cleaner (model PDC-002. Harrick Plasma Ithaca, NY/USA). Then, 3.5 ul of DHBc solution was pipetted onto the grids and they were plunge frozen in liquid ethane with a Vitrobot mark IV (FEI-Thermo Fisher Scientific). The settings for the Vitrobot were 3s blot time, 45 s wait time, blot force 0 at a temperature of 4 C and 100 % humidity

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	20251
Reported Resolution (Å)	3.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	77

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND
CTF CORRECTION	RELION
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	RELION
FINAL EULER ASSIGNMENT	RELION	3
CLASSIFICATION	RELION	3
RECONSTRUCTION	RELION	3.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		89241	particles were automatically selected using 2 D class averages as template