Poliovirus type 2 (strain MEF-1) stabilised virus-like particle (PV2 SC6b) from a yeast expression system.
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1EAH | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 12.078 |
| f_angle_d | 0.546 |
| f_chiral_restr | 0.044 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.003 |
| Sample |
|---|
| Poliovirus 2 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | 3ul of sample double blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 113853 |
| Reported Resolution (?) | 2.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Icosahedral symmetry applied to final reconstruction. Final maps were post-processed with an inverse B-factor of -86.1 Angstrom squared. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1EAH) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Initial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using pheni ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/?**2) | 35.12 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2300 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | DARK FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 150000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Calibrated pixel size was 0.831 A/pixel. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.5.3 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 4.5.3 |
| MODEL FITTING | UCSF Chimera | 1.16 |
| MODEL FITTING | Coot | 0.9.6 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.5.3 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.5.3 |
| CLASSIFICATION | cryoSPARC | 4.5.3 |
| RECONSTRUCTION | cryoSPARC | 4.5.3 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487-000 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 660747 | |||
