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CryoEM Structure of Zaire Ebola Virus Envelope Glycoprotein GP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JQ3
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.595 f_angle_d 0.589 f_chiral_restr 0.045 f_bond_d 0.004 f_plane_restr 0.004
Sample Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 foldon attached to stabilize soluble trimer
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 189700 Reported Resolution (Å) 3.05 Resolution Method FSC 0.143 CUT-OFF Other Details Non Uniform Refinement Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (5JQ3) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details Crystal Structure 5JQ3 was used as a starting model and fit with Chimera. Structure was further refined in Coot, Phenix, ChimeraX, Isolde
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 56.69
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.21.1_5286 MODEL REFINEMENT Coot MODEL REFINEMENT UCSF ChimeraX MODEL REFINEMENT ISOLDE
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 540665