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Cryo-EM structure of the DNA polymerase holoenzyme E9-A20-D4 of vaccinia virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OD8 experimental model Other PDBDEV_00000075 experimental model PDB 8HG1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.7263 f_angle_d 0.5974 f_chiral_restr 0.0427 f_bond_d 0.0049 f_plane_restr 0.0042
Sample E9-A20-D4 DNA polymerase holoenzyme
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 104239 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4od8, 8hg1) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Phenix real-space refinement
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 68
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1400 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 42000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.2.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC v4.2.1 MODEL FITTING UCSF Chimera 1.15 INITIAL EULER ASSIGNMENT cryoSPARC v4.2.1 FINAL EULER ASSIGNMENT cryoSPARC v4.2.1 CLASSIFICATION cryoSPARC v4.2.1 RECONSTRUCTION cryoSPARC v4.2.1 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 381864