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Cryo-EM structure of Hepatitis B virus surface antigen subviral particle with D2 symmetry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.308 f_angle_d 0.633 f_chiral_restr 0.042 f_plane_restr 0.005 f_bond_d 0.003
Sample Hepatitis B virus ayw/China/Tibet127/2002
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 113208 Reported Resolution (Å) 6.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D2
Map-Model Fitting and Refinement Id 1 2 Refinement Space REAL REAL Refinement Protocol RIGID BODY FIT FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 1800 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 22500 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION IMAGE ACQUISITION SerialEM MODEL FITTING UCSF Chimera 1.16 RECONSTRUCTION cryoSPARC MODEL FITTING iMODFIT 1.51 MODEL REFINEMENT PHENIX 1.20.1_4487:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 10324877