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SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 3up conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MY2 experimental model PDB 3K1K experimental model PDB 7KLW
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.125 f_angle_d 1.056 f_chiral_restr 0.067 f_plane_restr 0.008 f_bond_d 0.006
Sample SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 Sample Components SARS-CoV-2 spike protein sybody#15 and sybody#68
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 78933 Reported Resolution (Å) 2.98 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (7MY2, 3K1K, 7KLW) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 53
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 300 Maximum Defocus (nm) 2000 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 49407 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1.13 MODEL FITTING Coot 0.9-pre MODEL FITTING UCSF Chimera 0.93 INITIAL EULER ASSIGNMENT RELION 3.0.8 FINAL EULER ASSIGNMENT cryoSPARC 2.15.0 RECONSTRUCTION cryoSPARC 2.15.0 MODEL REFINEMENT PHENIX 1.18.2-3874-000
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 637105