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SARS-CoV-2 Spike in complex with neutralizing nanobody Nb6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VXX
Sample Complex of Spike S2P glycoprotein with synthetic nanobody Nb6 Sample Components Spike S2P glycoprotein synthetic nanobody Nb6
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 58493 Reported Resolution (Å) 3.03 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 FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 66
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 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM 3.8.0 CTF CORRECTION cryoSPARC 2.15.0 MODEL REFINEMENT PHENIX 1.18.2-3874 FINAL EULER ASSIGNMENT cisTEM 1.0.0 RECONSTRUCTION cisTEM 1.0.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Performed at reconstruction stage as is standard for cryoSPARC 2033067