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One RBD up state of Spike glycoprotein, SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D56
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.47 f_angle_d 0.641 f_chiral_restr 0.047 f_bond_d 0.005 f_plane_restr 0.004
Sample Spike glycoprotein, SARS-CoV-2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot force, 0
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 261703 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8d56) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 84.6 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 25
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1800 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 75000 Calibrated Magnification 130841 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 CTF CORRECTION RELION 3.1 MODEL FITTING UCSF Chimera 1.15 MODEL FITTING Coot 0.9.5 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.15 MODEL REFINEMENT REFMAC 5.8.0411
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION