Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to target RNA with non-complementary PFS
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.612 |
| f_angle_d | 0.594 |
| f_chiral_restr | 0.044 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Type III-Bv CRISPR complex from Dissulfurispira thermophila bound to target RNA with a non-complementary PFS |
| 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 | 358511 |
| Reported Resolution (Å) | 2.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final reconstruction generated by non-uniform refinement with per particle CTF correction enabled. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | ChimeraX's fit in map command was used to fit Alphafold predicted structure of individual subunits followed by refinement in PHENIX and manual editing ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 65 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 500 |
| 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 | 45000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.7.1 |
| IMAGE ACQUISITION | SerialEM | 4.2.0 |
| CTF CORRECTION | cryoSPARC | 4.7.1 |
| MODEL FITTING | UCSF ChimeraX | 1.10.1 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.7.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.7.1 |
| CLASSIFICATION | cryoSPARC | 4.7.1 |
| RECONSTRUCTION | cryoSPARC | 4.7.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 3264182 | Particles picked using a de novo template generated in CryoSPARC live that contained 329559 particles. | ||
