Activated wild-type SgrAI endonuclease DNA-bound dimer with Mg2+ and cleaved primary site DNA
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6OBJ | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 21.324 |
| f_angle_d | 0.491 |
| f_chiral_restr | 0.04 |
| f_bond_d | 0.004 |
| f_plane_restr | 0.004 |
| Sample |
|---|
| Activated wild-type filamentous SgrAI endonuclease with Mg2+ and cleaved primary site DNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 202664 |
| Reported Resolution (Å) | 3.05 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C2 |
| Axial Rise | 21.3 |
| Angular Rotation | -86.2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6OBJ) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 87.9 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 29.6 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2000 |
| 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 | 165000 |
| Calibrated Magnification | 60240 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | cryoSPARC | |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | |
| FINAL EULER ASSIGNMENT | RELION | 4.2 |
| RECONSTRUCTION | cryoSPARC | 4.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
