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Trimeric HSV-2F gB ectodomain in postfusion conformation with three bound HDIT101 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_long_range_B_refined 33.292 r_long_range_B_other 33.292 r_scangle_other 21.231 r_mcangle_it 17.872 r_mcangle_other 17.871 r_dihedral_angle_3_deg 15.452 r_scbond_it 12.604 r_scbond_other 12.603 r_mcbond_it 10.961 r_mcbond_other 10.961
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 33.292 r_long_range_B_other 33.292 r_scangle_other 21.231 r_mcangle_it 17.872 r_mcangle_other 17.871 r_dihedral_angle_3_deg 15.452 r_scbond_it 12.604 r_scbond_other 12.603 r_mcbond_it 10.961 r_mcbond_other 10.961 r_dihedral_angle_2_deg 7.043 r_dihedral_angle_1_deg 5.121 r_angle_refined_deg 1.073 r_angle_other_deg 0.373 r_chiral_restr 0.047 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 Trimeric HSV-2G gB ectodomain in post-fusion conformation with three bound HDIT101 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 234096 Reported Resolution (Å) 3.45 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 K3 (6k x 4k) Electron Dose (electrons/Å**2) 1.325
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS 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) 200 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 6289845