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Structure of Japanese encephalitis virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J57
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.961 f_angle_d 1.08 f_chiral_restr 0.051 f_bond_d 0.011 f_plane_restr 0.006
Sample Japanese encephalitis virus
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details blot for 3 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 15260 Reported Resolution (Å) 4.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (3J57) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Correlation coefficient Overall B Value 120 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 1.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI POLARA 300 Minimum Defocus (nm) 1200 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode BRIGHT FIELD Specimen Holder Model OTHER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EMAN 2.0 IMAGE ACQUISITION RELION 1.3 CTF CORRECTION Gctf 5.0 MODEL FITTING CHIMERA 2.0 INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION 1.3 CLASSIFICATION RELION 1.3 RECONSTRUCTION RELION 1.3 MODEL REFINEMENT PHENIX 3.O
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 22000