5O5P
Poliovirus type 3 (strain Saukett) stabilized virus-like particle in complex with the pocket factor compound GPP3
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 9.41 |
| f_angle_d | 0.785 |
| f_chiral_restr | 0.053 |
| f_plane_restr | 0.007 |
| f_bond_d | 0.006 |
| Sample |
|---|
| Human poliovirus 3 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot for 4 seconds before plunging. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 2060 |
| Reported Resolution (Å) | 4.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| 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 | phenix.real_space_refine was used to refine the atomic model in the cryo-em map. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1.2 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2800 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | 37037 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminary grid screening was performed. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | ETHAN | 1.2 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | RELION | 1.3 |
| MODEL FITTING | UCSF Chimera | 1.12 |
| INITIAL EULER ASSIGNMENT | RELION | 1.3 |
| FINAL EULER ASSIGNMENT | RELION | 1.3 |
| CLASSIFICATION | RELION | 1.3 |
| RECONSTRUCTION | RELION | 1.3 |
| MODEL REFINEMENT | PHENIX | 1.12rc0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF parameters were estimated using CTFFIND3 as part of RELION 1.3. | 6639 | Automated particle picking (ETHAN) was followed by manual cleaning (EMAN2). | |
