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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9BH7
pdb_00009bh7
10.2210/pdb9bh7/pdb
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FASTA
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MMCIF
Binary MMCIF
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Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
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Binary MMCIF Zipped(.gz)
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Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Human DNA polymerase theta helicase domain
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 pool cooled by liquid nitrogen using a manual plunge freezer.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
138712
Reported Resolution (Å)
3.5
Resolution Method
FSC 0.143 CUT-OFF
Other Details
We performed local refinement of a single protomer, and then multiplied the output protomer map to fit the C2 symmetric dimer map.
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
55.33
Fitting Procedure
?
Details
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 two protomers into the dimer map.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å
2
)
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
MODEL REFINEMENT
PHENIX
1.20.1
INITIAL EULER ASSIGNMENT
cryoSPARC
4.3
FINAL EULER ASSIGNMENT
cryoSPARC
4.3
CLASSIFICATION
cryoSPARC
4.3
RECONSTRUCTION
cryoSPARC
4.3
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
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