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CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with neutralizing fabs 2C12, 7I13 and 13H11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VOB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.06 f_angle_d 0.624 f_chiral_restr 0.043 f_plane_restr 0.007 f_bond_d 0.003
Sample Pentameric complex of HCMV proteins gH, gL, UL128, UL130, UL131A bound to fabs of human neutralizing antibodies 2C12, 7I13 and 13H11
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details blot for 3.5s before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 4792984 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details A composite map was generated from the three individual focused 3D maps using phenix combine_focused_maps Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5VOB) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 58
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch 0.56 IMAGE ACQUISITION SerialEM 3.7.11 CTF CORRECTION CTFFIND 4.1.13 MODEL FITTING Coot 0.89 MODEL REFINEMENT PHENIX 1.19.2 INITIAL EULER ASSIGNMENT cisTEM 1.02 FINAL EULER ASSIGNMENT cisTEM 1.02 CLASSIFICATION RELION 3.1 RECONSTRUCTION cisTEM 1.02
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5128264 template-matching particle picking