☰ Navigation Tabs
SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KDL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.869 f_angle_d 0.657 f_chiral_restr 0.053 f_plane_restr 0.006 f_bond_d 0.004
Sample SARS-CoV-2 S-GSAS-Omicron Spike Ectodomain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 328521 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7KDL) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU MODEL REFINEMENT PHENIX CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION Coot RECONSTRUCTION ISOLDE RECONSTRUCTION PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION