Skip to main content

 9BH9 | pdb_00009bh9

Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology aligning conformation


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A9J 
experimental modelPDB 2P6R 
Sample
Human DNA polymerase theta helicase domain bound to stem-loop DNA with microhomology in the 3' overhang
Sample Components
Human DNA polymerase theta helicase domain
Stem-loop DNA with microhomology in the 3' overhang
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Details3 microliters of sample was applied to the surface of the grid, blotted for 2 seconds after the liquid spot on the filter paper stopped spreading, and ...3 microliters of sample was applied to the surface of the grid, blotted for 2 seconds after the liquid spot on the filter paper stopped spreading, and the grid was plunged into a liquid ethane bath cooled by liquid nitrogen.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles107353
Reported Resolution (Å)3.5
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNon-uniform refinement and local filtering by resolution
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (5A9J, 2P6R)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value67.19
Fitting Procedure
DetailsWe modeled DNA bases into sharpened density when possible. We modeled the DNA backbone into locally filtered density in low resolution areas.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k 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)1000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification60024
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.3
IMAGE ACQUISITIONLeginon3.6
CTF CORRECTIONcryoSPARC4.3
MODEL FITTINGUCSF ChimeraX1.6.1
MODEL FITTINGISOLDE1.6.0
INITIAL EULER ASSIGNMENTcryoSPARC4.3
FINAL EULER ASSIGNMENTcryoSPARC4.3
CLASSIFICATIONcryoSPARC4.3
RECONSTRUCTIONcryoSPARC4.3
MODEL REFINEMENTPHENIX1.20.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION5424691