5IRE
The cryo-EM structure of Zika Virus
ELECTRON MICROSCOPY
| Sample |
|---|
| Zika virus |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | GATAN CRYOPLUNGE 3 |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot for 5 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 11842 |
| Reported Resolution (?) | 3.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Soft mark was applied to the even/odd map before FSC calculation. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | T = Tmap + weight * TrestraintsT = Tmap + weight * Trestraints | ||||
| Overall B Value | 150 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/?**2) | 23 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2500 |
| 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 | 14000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Appion | 3.2 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | CTFFIND | 3 |
| MODEL REFINEMENT | PHENIX | 1.10.1-2155 |
| INITIAL EULER ASSIGNMENT | jspr | 2015 |
| FINAL EULER ASSIGNMENT | jspr | 2015 |
| CLASSIFICATION | jspr | 2015 |
| RECONSTRUCTION | jspr | 2015 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | Phase flipping was performed during 3D reconstruction. | 64518 | Particles were picked from 2-binned images using the template-picking method from Appion. | |
