Tetrameric POLQ Helicase-like Domain Bound to Cmpd 36, a Small-Molecule ATPase Inhibitor and Drug Candidate Analog
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5AGA | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.068 |
| f_angle_d | 0.498 |
| f_chiral_restr | 0.037 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| Polymerase theta N-terminal domain in complex with ATPase inhibitor compound |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 microL drop of sample suspension is applied to an EM grid that has been plasma-cleaned using a Gatan Solarus. After blotting the sample away with fi ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 387000 |
| Reported Resolution (Å) | 2.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5AGA) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | CC_mask: 0.7952 | ||||
| Overall B Value | 112.5 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 53 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 1500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.1 |
| IMAGE ACQUISITION | Leginon | |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | 1.19.2_4158 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ~2.5M particles were initially selected from 4985 manually curated micrographs using cryoSPARC 3.1 live. All subsequent data processing was carried out in cryoSPARC 3.1.These particles were subjected to 3 rounds of 2D classification. A subset of particles from the final round of 2D classification were used to train the Deep Learning particle picker Topaz (as implemented in cryoSPARC 3.1). The Topaz trained model was used to re-extract particles from the 4985 micrographs, yielding a new particle set comprising 387k particles. | |||
