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Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KDL experimental model PDB 7JMO
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.633 f_angle_d 1.765 f_chiral_restr 0.092 f_bond_d 0.013 f_plane_restr 0.013
Sample Spike protein Trimer; Mink/Cluster 5 variant
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 346973 Reported Resolution (Å) 2.94 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7KDL, 7JMO) Refinement Space Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 52.9
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 Coot MODEL FITTING UCSF Chimera MODEL REFINEMENT ISOLDE MODEL REFINEMENT UCSF Chimera
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION