Cryo-EM structure of cGAS tetramer in complex with BuDNA (bubble DNA)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7UUX | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 25.386 |
| f_angle_d | 0.528 |
| f_chiral_restr | 0.035 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.003 |
| Sample |
|---|
| The structure of mouse cGAS in complex with a bubble DNA |
| Sample Components |
| mouse cGAS |
| The forward strand of bubble DNA |
| The reverse strand of bubble DNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Filter paper blotted with blot force 2 and blot time 2s, and plunge-frozen in liquid ethane using a Vitrobot Mark IV at 4 degree Celsius and 100% humi ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 62441 |
| Reported Resolution (Å) | 3.48 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Particles are randomly split into two halves. |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5N6I, 5N6I, 5N6I, 5N6I, 5N6I, 5N6I, 5N6I, 5N6I) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 87.5 | ||||
| Fitting Procedure | |||||
| Details | Initial local fitting was done using UCSF ChimeraX, and then COOT was used for manual building. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 1800 |
| 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 | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v4.3.1 |
| IMAGE ACQUISITION | EPU | 1.12 - 3.7 |
| CTF CORRECTION | cryoSPARC | v4.3.1 |
| MODEL FITTING | UCSF ChimeraX | version 1.9 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v4.3.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v4.3.1 |
| CLASSIFICATION | cryoSPARC | v4.3.1 |
| RECONSTRUCTION | cryoSPARC | v4.3.1 |
| MODEL REFINEMENT | PHENIX | 1.18.2_3874: |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2969717 | A total of 2,969,717 particles were auto-picked using Blob Picker in CryoSPARC. | ||
