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Structure of SARS-CoV-1 Spike Protein with Engineered x2 Disulfide (G400C and V969C), Locked-2 Conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XTZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.578 f_angle_d 0.758 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.006
Sample SARS-CoV-1 spike protein
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 192457 Reported Resolution (Å) 3.44681 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7XTZ) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 28 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 62
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 2400 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 45000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION SerialEM 3.8.7 CTF CORRECTION RELION 3.1 MODEL FITTING UCSF Chimera 1.16 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.19.1_4122
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 967643 Particles were picked by Warp v1.09