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Duck hepatitis B virus capsid Mutant R124E_delta78-122
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
12.606
f_angle_d
0.536
f_chiral_restr
0.034
f_bond_d
0.003
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 dischargi ...
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
44498
Reported Resolution (Å)
3
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
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)
60
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
INITIAL EULER ASSIGNMENT
RELION
FINAL EULER ASSIGNMENT
RELION
3
CLASSIFICATION
RELION
3
RECONSTRUCTION
RELION
3.0
MODEL REFINEMENT
PHENIX
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
74760
particles were automatically selected using 2 D class averages as template