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Structure of SARS-CoV-2 spike RBD in complex with NT-108 scFv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YK4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.544 f_angle_d 0.592 f_chiral_restr 0.046 f_plane_restr 0.005 f_bond_d 0.004
Sample SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv Sample Components SARS-CoV-2 spike glycoprotein NT-108 scFv
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blotting time 5 s and blotting force 5.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 124137 Reported Resolution (Å) 3.27 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8YK4) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 53.52
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION EPU CTF CORRECTION RELION 3.1 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 652138