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Cryo-EM structure of coxsackievirus A6 mature virion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XS4
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.01 r_long_range_B_refined 20.96 r_long_range_B_other 20.96 r_dihedral_angle_4_deg 15.267 r_mcangle_it 14.59 r_mcangle_other 14.59 r_dihedral_angle_3_deg 13.134 r_scangle_other 12.954 r_mcbond_it 10.258 r_mcbond_other 10.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.01 r_long_range_B_refined 20.96 r_long_range_B_other 20.96 r_dihedral_angle_4_deg 15.267 r_mcangle_it 14.59 r_mcangle_other 14.59 r_dihedral_angle_3_deg 13.134 r_scangle_other 12.954 r_mcbond_it 10.258 r_mcbond_other 10.257 r_scbond_other 9.006 r_scbond_it 9.005 r_dihedral_angle_1_deg 6.58 r_angle_refined_deg 1.572 r_angle_other_deg 1.284 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Sample Components Capsid
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 1769 Reported Resolution (Å) 2.68 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (5XS4) Refinement Space RECIPROCAL Refinement Protocol RIGID BODY FIT Refinement Target correlation coefficient Overall B Value 66 Fitting Procedure Details iterative cycles of building - real space refinement - reciprocal space refinement
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION EPU 1.12 CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera MODEL REFINEMENT Coot 0.9.5 MODEL REFINEMENT PHENIX 1.19.2 MODEL REFINEMENT REFMAC 5 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 211991