ELECTRON MICROSCOPY

Sample

Human DNA polymerase theta helicase domain bound to stem-loop DNA with microhomology in the 3' overhang

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details 3 microliters of sample was applied to the surface of the grid, blotted with Whatman 1 filter paper until 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 Method SINGLE PARTICLE
Number of Particles 102983
Reported Resolution (Å) 3.6
Resolution Method FSC 0.143 CUT-OFF
Other Details Non-uniform refinement and local filtering by resolution
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Cross-correlation coefficient
Overall B Value 69.39
Fitting Procedure ?
Details We modeled DNA bases into sharpened density when possible. We modeled the DNA backbone into locally filtered density in low resolution areas.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 50
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 1000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 105000
Calibrated Magnification 60024
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.3
IMAGE ACQUISITION Leginon 3.6
CTF CORRECTION cryoSPARC 4.3
MODEL FITTING UCSF ChimeraX 1.6.1
MODEL FITTING ISOLDE 1.6.0
INITIAL EULER ASSIGNMENT cryoSPARC 4.3
FINAL EULER ASSIGNMENT cryoSPARC 4.3
CLASSIFICATION cryoSPARC 4.3
RECONSTRUCTION cryoSPARC 4.3
MODEL REFINEMENT PHENIX 1.20.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?