6ZY6

Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in State 2


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GWK 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.687
f_angle_d1.06
f_chiral_restr0.078
f_bond_d0.01
f_plane_restr0.007
Sample
Etoposide-bound Human Top2a DNA-binding/cleavage domain in state 2
Sample Components
DNA topoisomerase 2-alpha
DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles39368
Reported Resolution (Å)4.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (5GWK)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.01
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctf
CTF CORRECTIONRELION3.1
CTF CORRECTIONcryoSPARCv3
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTcryoSPARCv3
FINAL EULER ASSIGNMENTcryoSPARCv3
RECONSTRUCTIONcryoSPARCv3
MODEL REFINEMENTPHENIX1.18rc4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1908092