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Cryo-EM structure of a coxsackievirus A6 virus-like particle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YHQ
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 38.102 r_long_range_B_other 38.101 r_scangle_other 29.925 r_mcangle_it 24.679 r_mcangle_other 24.675 r_scbond_it 21.63 r_scbond_other 21.625 r_dihedral_angle_2_deg 19.813 r_dihedral_angle_3_deg 19.743 r_mcbond_it 17.547
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 38.102 r_long_range_B_other 38.101 r_scangle_other 29.925 r_mcangle_it 24.679 r_mcangle_other 24.675 r_scbond_it 21.63 r_scbond_other 21.625 r_dihedral_angle_2_deg 19.813 r_dihedral_angle_3_deg 19.743 r_mcbond_it 17.547 r_mcbond_other 17.53 r_dihedral_angle_1_deg 6.265 r_angle_refined_deg 1.52 r_angle_other_deg 0.5 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_4_deg 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 Coxsackievirus A6 virus-like particle
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Blotting for 10 seconds from the carbon side
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 44582 Reported Resolution (Å) 3.15 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (5yhq, 5yhq, 5yhq) Refinement Space RECIPROCAL Refinement Protocol FLEXIBLE FIT Refinement Target Average FSC Overall B Value 130 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 58.24
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL 3200FSC Minimum Defocus (nm) 500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 4.1 Imaging Mode BRIGHT FIELD Specimen Holder Model JEOL 3200FSC CRYOHOLDER Nominal Magnification 40000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.1.1 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4.1.1 MODEL FITTING Coot 0.9.5 INITIAL EULER ASSIGNMENT cryoSPARC 4.1.1 FINAL EULER ASSIGNMENT cryoSPARC 4.1.1 CLASSIFICATION cryoSPARC 4.1.1 RECONSTRUCTION cryoSPARC 4.1.1 MODEL REFINEMENT REFMAC 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 62219