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Cryo-EM structure of the entire Human topoisomerase II alpha in State 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GWK experimental model PDB 1ZXM
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.424 f_angle_d 0.975 f_chiral_restr 0.116 f_bond_d 0.009 f_plane_restr 0.006
Sample Etoposide-bound Entire Human Top2a in state 2 Sample Components DNA topoisomerase 2-alpha DNA
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 13420 Reported Resolution (Å) 7.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5GWK, 1ZXM) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 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 SerialEM CTF CORRECTION Gctf CTF CORRECTION RELION 3.1 CTF CORRECTION cryoSPARC v3 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC v3 FINAL EULER ASSIGNMENT cryoSPARC v3 RECONSTRUCTION cryoSPARC v3 MODEL REFINEMENT PHENIX 1.18rc4
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1908092