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CryoEM structure of M. mazei topoisomerase VI(A-E342Q)-minicircle DNA complex in cleavage state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other experimental model PDB 2Q2E
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.4671 f_angle_d 0.7383 f_chiral_restr 0.0478 f_plane_restr 0.0057 f_bond_d 0.0037
Sample Topoisomerase VI heterotetramer (A2B2) bound to minicircle DNA and ADPNP Sample Components Top6 heterotetramer (A2B2) 306 bp minicircle DNA
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Vitrification carried out in air
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 329731 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (2Q2E) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 30
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.9.6 CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING Coot 0.9.8.91 MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING ISOLDE 1.9 MODEL REFINEMENT PHENIX 1.21.1_5286 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.0 RECONSTRUCTION EMReady 2.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2479118