8PVV
Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 30 nt RNA guide and 51 nt DNA target
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8OK9 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 19.032 |
| f_angle_d | 0.565 |
| f_chiral_restr | 0.043 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.003 |
| Sample |
|---|
| AfAgo and AfAgo-N complex with 30 nt RNA guide and 51 nt DNA target |
| Sample Components |
| Piwi protein |
| Archaeoglobus fulgidus AfAgo-N protein |
| RNA (30-MER) |
| DNA (51-MER) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 498038 |
| Reported Resolution (Å) | 2.81 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8ok9, 8ok9) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 31 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS GLACIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | 92000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v.4.2.1 |
| MODEL REFINEMENT | PHENIX | 1.18.2_3874: |
| IMAGE ACQUISITION | EPU | |
| MASKING | UCSF Chimera | 1.17.1 |
| CTF CORRECTION | cryoSPARC | v.4.2.1 |
| MODEL FITTING | UCSF Chimera | 1.17.1 |
| OTHER | Coot | 0.9 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v.4.2.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v.4.2.1 |
| CLASSIFICATION | cryoSPARC | v.4.2.1 |
| RECONSTRUCTION | cryoSPARC | v.4.2.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 2326555 | Blob particle picking | ||
