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CryoEM structure of human enterovirus 70 native virion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MW8
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 51.257 r_long_range_B_other 51.253 r_scangle_other 40.798 r_scbond_it 38.035 r_scbond_other 38.03 r_mcangle_it 34.472 r_mcangle_other 34.469 r_mcbond_other 32.719 r_mcbond_it 32.712 r_dihedral_angle_2_deg 31.793
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 51.257 r_long_range_B_other 51.253 r_scangle_other 40.798 r_scbond_it 38.035 r_scbond_other 38.03 r_mcangle_it 34.472 r_mcangle_other 34.469 r_mcbond_other 32.719 r_mcbond_it 32.712 r_dihedral_angle_2_deg 31.793 r_dihedral_angle_4_deg 22.236 r_dihedral_angle_3_deg 12.725 r_dihedral_angle_1_deg 6.324 r_angle_other_deg 2.287 r_angle_refined_deg 1.772 r_chiral_restr 0.096 r_bond_other_d 0.035 r_bond_refined_d 0.018 r_gen_planes_other 0.013 r_gen_planes_refined 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
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 6390 Reported Resolution (Å) 2.63 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (4MW8) Refinement Space RECIPROCAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value 43 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 48
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 1.5 IMAGE ACQUISITION EPU 1.8 CTF CORRECTION Gctf CTF CORRECTION RELION 3.1 MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION RELION 10524 autopicking using crYOLO