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apPol-DNA-nucleotide complex (ternary 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DKT
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.026 f_angle_d 0.697 f_chiral_restr 0.046 f_bond_d 0.005 f_plane_restr 0.004
Sample Ternary complex of apicoplast DNA polymerase, DNA and dGTP with Ca2+
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 92787 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5DKT) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 3800 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 81000 Calibrated Magnification 81000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU 3.9.1 CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC 4.5.1 FINAL EULER ASSIGNMENT cryoSPARC 4.5.1 RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.20.1_4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1993221