3J6U
Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab
ELECTRON MICROSCOPY
| Sample |
|---|
| Dengue virus 3 complexed with human antibody 5J7 Fab |
| Sample Components |
| Dengue virus 3 |
| Fab 5J7 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blotted with filter paper for 2 seconds prior to snap freezing in liquid ethane (FEI VITROBOT MARK IV) |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 970 |
| Reported Resolution (Å) | 9 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | (Single particle details: Particles were manually selected.) (Single particle--Applied symmetry: I) |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3J6T, 3J6T, 3J6T, 3J6T, 3J6T, 3J6T, 3MA9, 1DEE) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | real space correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--flexible DETAILS--Initially fitted in Chimera, model rebuilt in Coot, refined in NAMD/MDFF | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON I (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 18 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2012-03-23 |
| Temperature (Kelvin) | 100 |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 4200 |
| 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 | 59000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Coot | |
| MODEL FITTING | MDFF | |
| MODEL FITTING | NAMD | |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | EMAN | 1 |
| RECONSTRUCTION | EMAN | 2 |
| RECONSTRUCTION | MPSA | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| each particle | ||||
