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CryoEM structure of Ageratum Yellow Vein virus (AYVV)
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.321 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_4_deg 13.383 r_dihedral_angle_1_deg 6.752 r_long_range_B_refined 6.386 r_long_range_B_other 6.386 r_scangle_other 3.682 r_mcangle_it 3.058 r_mcangle_other 3.058 r_scbond_it 2.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.321 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_4_deg 13.383 r_dihedral_angle_1_deg 6.752 r_long_range_B_refined 6.386 r_long_range_B_other 6.386 r_scangle_other 3.682 r_mcangle_it 3.058 r_mcangle_other 3.058 r_scbond_it 2.028 r_scbond_other 2.028 r_mcbond_it 1.739 r_mcbond_other 1.738 r_angle_other_deg 1.399 r_angle_refined_deg 1.088 r_chiral_restr 0.084 r_bond_refined_d 0.006 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 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 Ageratum yellow vein virus
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 64932 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D5
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 110
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2700 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 IMAGE ACQUISITION EPU 1.7 CTF CORRECTION Gctf 0.5 MODEL FITTING Coot 0.8.8 INITIAL EULER ASSIGNMENT RELION 2.0 FINAL EULER ASSIGNMENT RELION 2.1 CLASSIFICATION RELION 2.1 RECONSTRUCTION RELION 2.1 MODEL REFINEMENT PHENIX 1.11 MODEL REFINEMENT REFMAC 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 116240