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CryoEM structure of M. mazei topoisomerase VI-minicircle DNA complex in asymmetric state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q2E other Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.27 f_angle_d 1.1476 f_chiral_restr 0.0595 f_plane_restr 0.0109 f_bond_d 0.0067
Sample Topoisomerase VI heterotetramer (A2B2) bound to minicircle DNA and ADPNP Sample Components Top6 heterotetramer (A2B2) 327 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 293857 Reported Resolution (Å) 3.8 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 FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 46
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 130000 Calibrated Magnification 130000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.9 IMAGE ACQUISITION EPU 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 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1 RECONSTRUCTION EMReady 2.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5216613