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Cryo-EM structure of trimeric prME spike of Spondweni virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZQI
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.74 f_angle_d 0.539 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.002
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 305017 Reported Resolution (Å) 4.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6ZQI) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 30
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 Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION Gctf 1.06 FINAL EULER ASSIGNMENT RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.17.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2572800 2572800 sub-particles were generated from 42880 immature Spondweni virions (selected in cryoSPARC) via localised reconstruction