ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5YHQ | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 38.102 |
| r_long_range_B_other | 38.101 |
| r_scangle_other | 29.925 |
| r_mcangle_it | 24.679 |
| r_mcangle_other | 24.675 |
| r_scbond_it | 21.63 |
| r_scbond_other | 21.625 |
| r_dihedral_angle_2_deg | 19.813 |
| r_dihedral_angle_3_deg | 19.743 |
| r_mcbond_it | 17.547 |
| Sample |
|---|
| Coxsackievirus A6 virus-like particle |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blotting for 10 seconds from the carbon side |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 44582 |
| Reported Resolution (Å) | 3.15 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5yhq, 5yhq, 5yhq) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Average FSC | ||||
| Overall B Value | 130 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 58.24 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL 3200FSC |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 4.1 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | JEOL 3200FSC CRYOHOLDER |
| Nominal Magnification | 40000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.1.1 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | 4.1.1 |
| MODEL FITTING | Coot | 0.9.5 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.1.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.1.1 |
| CLASSIFICATION | cryoSPARC | 4.1.1 |
| RECONSTRUCTION | cryoSPARC | 4.1.1 |
| MODEL REFINEMENT | REFMAC | 5 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 62219 | |||
