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Trimeric HSV-1F gB ectodomain in postfusion conformation with three bound HDIT102 Fab molecules.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GUM
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.053 r_long_range_B_refined 6.903 r_long_range_B_other 6.903 r_dihedral_angle_1_deg 4.557 r_dihedral_angle_2_deg 3.915 r_scangle_other 3.771 r_mcangle_it 3.329 r_mcangle_other 3.329 r_scbond_it 2.176 r_scbond_other 2.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.053 r_long_range_B_refined 6.903 r_long_range_B_other 6.903 r_dihedral_angle_1_deg 4.557 r_dihedral_angle_2_deg 3.915 r_scangle_other 3.771 r_mcangle_it 3.329 r_mcangle_other 3.329 r_scbond_it 2.176 r_scbond_other 2.176 r_mcbond_it 1.97 r_mcbond_other 1.969 r_angle_refined_deg 1.106 r_angle_other_deg 0.537 r_bond_other_d 0.012 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_dihedral_angle_4_deg r_chiral_restr 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 Trimeric HSV-1F gB ectodomain in post-fusion conformation with three bound HDIT102 Fab molecules
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 208280 Reported Resolution (Å) 3.44 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (2gum) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 1.15
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 4.0 IMAGE ACQUISITION SerialEM 3.8 CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING CCP4 package 1.6 INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0 MODEL REFINEMENT CCP4 package 1.6
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1059496