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Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Closed State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VXX
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.752 f_angle_d 1.026 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.006
Sample Disulphide-stabilized SARS-CoV-2 Spike protein 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 210946 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (6VXX) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target correlation coefficient Overall B Value 116 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM 3.8 CTF CORRECTION CTFFIND 4.1.13 MODEL FITTING Coot 0.9 MODEL REFINEMENT PHENIX 1.18.2 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 587351 template picking