7Y0D
Cryo-EM structure of the Mycobacterium smegmatis DNA integrity scanning protein (MsDisA).
ELECTRON MICROSCOPY
| Sample |
|---|
| Cryo-EM structure of the Mycobacterium smegmatis DNA integrity scanning protein (MsDisA). |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blotted for 3.5s |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 204932 |
| Reported Resolution (Å) | 3.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | 138.7 | ||||
| Fitting Procedure | |||||
| Details | Model from AlphaFold was used as the starting point (AF-A0R564-F1-model_v2.pdb). | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 27.75 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 2100 |
| Maximum Defocus (nm) | 3300 |
| 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 | 75000 |
| Calibrated Magnification | 130841 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.0 |
| IMAGE ACQUISITION | EPU | |
| MODEL FITTING | Coot | 0.9.5 |
| MODEL FITTING | UCSF Chimera | 1.15 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.0 |
| RECONSTRUCTION | cryoSPARC | 3.0 |
| MODEL REFINEMENT | PHENIX | 1.19 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 973755 | Template Picker from cryoSparc 3.0 were used to pick total particles in the first extraction. Three rounds of reference-free 2d classification were carried to remove bad particles followed by NU-refinement. | ||
