9BH6
Human DNA polymerase theta helicase domain tetramer in the apo form
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5A9J | |
| Sample |
|---|
| Human DNA polymerase theta helicase domain |
| Specimen Preparation | |
|---|---|
| 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 filte ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 208545 |
| Reported Resolution (Å) | 3.3 |
| 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 D2 symmetric tetramer map. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5A9J) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 54.43 | ||||
| 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 ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k 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) | 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 |
| EM Software | ||
|---|---|---|
| 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 | 1474207 | |||
