Cryo-EM structure of His6-tagged D13 assembled into scaffold-like particles from vaccinia virus
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.554 |
| f_angle_d | 0.637 |
| f_chiral_restr | 0.051 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.005 |
| Sample |
|---|
| Assembled scaffold-like particle of Vaccinia virus D13 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Wait time: 10sec Blot force: 0 Blot time: 5sec |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 722411 |
| Reported Resolution (Å) | 2.88 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Map-to-model correlation | ||||
| Overall B Value | 173.77 | ||||
| Fitting Procedure | |||||
| Details | Model building was proceeded by manually fitting the cryo-EM structure of D13 (PDB ID 7VFD) into our cryo-EM map using UCSF Chimera. The model was su ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOCONTINUUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 38.6 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 42000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.5.3 |
| CTF CORRECTION | cryoSPARC | 4.5.3 |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | Coot | 0.9.8.92 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.5.3 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.5.3 |
| CLASSIFICATION | cryoSPARC | 4.5.3 |
| RECONSTRUCTION | cryoSPARC | 4.5.3 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
