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Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZGE
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.726 f_angle_d 0.587 f_chiral_restr 0.054 f_plane_restr 0.005 f_bond_d 0.003
Sample Ectodomain of S1 protein from SARS-CoV-2 expressed in HEK cells and purified. Sample in the presence of excess biliverdin.
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 181126 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6ZGE) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 33
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 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 MODEL FITTING UCSF Chimera RECONSTRUCTION cryoSPARC 2 MODEL REFINEMENT PHENIX 1.19rc5-4047
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION