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SARS-CoV-2 S protein S:A222V + S:D614G mutant 1-up
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BNN
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.394 r_long_range_B_refined 18.718 r_long_range_B_other 18.718 r_dihedral_angle_3_deg 15.483 r_dihedral_angle_4_deg 13.711 r_mcangle_it 7.001 r_mcangle_other 7.001 r_scangle_other 5.597 r_dihedral_angle_1_deg 3.821 r_mcbond_it 3.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.394 r_long_range_B_refined 18.718 r_long_range_B_other 18.718 r_dihedral_angle_3_deg 15.483 r_dihedral_angle_4_deg 13.711 r_mcangle_it 7.001 r_mcangle_other 7.001 r_scangle_other 5.597 r_dihedral_angle_1_deg 3.821 r_mcbond_it 3.809 r_mcbond_other 3.809 r_scbond_it 2.88 r_scbond_other 2.88 r_angle_refined_deg 1.619 r_angle_other_deg 1.361 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample SARS-CoV-2 S protein S:A222V + S:D614G mutant
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 145681 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7BNN) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 32.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 300 Maximum Defocus (nm) 3500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode OTHER Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 120000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO PARTICLE SELECTION Scipion IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND CTF CORRECTION Gctf CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera MODEL FITTING Coot MODEL REFINEMENT REFMAC INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION RELION CLASSIFICATION Scipion RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 509466