6ZY8
Cryo-EM structure of the entire Human topoisomerase II alpha in State 2
ELECTRON MICROSCOPY
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 |
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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 |