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Cryo-EM structure of the Strand displacement Complex (II) of Yeast Mitochondrial DNA polymerase Gamma (MIP1) with downstream DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P15801-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.545 f_angle_d 0.736 f_chiral_restr 0.047 f_plane_restr 0.007 f_bond_d 0.003
Sample Cryo-EM map of the Strand displacement Complex (III) of Yeast Mitochondrial DNA polymerase Gamma (MIP1)
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 137107 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 60
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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU 3.7 MODEL FITTING Coot 0.9.8.5 RECONSTRUCTION cryoSPARC 4.4 MODEL REFINEMENT PHENIX 1.21rc1_5127
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF estimation in cryoSPARC. 9600000