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 9BH6 | pdb_00009bh6

Human DNA polymerase theta helicase domain tetramer in the apo form


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A9J 
Sample
Human DNA polymerase theta helicase domain
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 with Whatman 1 filter paper until 2 seconds after the liquid spot on the filte ...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 pool cooled by liquid nitrogen using a manual plunge freezer.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles208545
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsWe performed local refinement of a single protomer and then multiplied the output protomer map to fit the D2 symmetric tetramer map.
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1 (5A9J)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value54.43
Fitting Procedure
DetailsWe used ISOLDE to flexibly fit one protomer into the locally refined protomer map. The output protomer model was multiplied and we used ISOLDE to fit ...We used ISOLDE to flexibly fit one protomer into the locally refined protomer map. The output protomer model was multiplied and we used ISOLDE to fit four protomers into the tetramer map.
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
MODEL REFINEMENTPHENIX1.20.1
INITIAL EULER ASSIGNMENTcryoSPARC4.3
FINAL EULER ASSIGNMENTcryoSPARC4.3
CLASSIFICATIONcryoSPARC4.3
RECONSTRUCTIONcryoSPARC4.3
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1474207