ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3J6R | |
| Sample |
|---|
| Quasi-HPV16 complexed with H16.U4 Fab |
| Sample Components |
| Human papillomavirus |
| H16.U4 antibody |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | GATAN CRYOPLUNGE 3 |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Plunged into liquid ethane (GATAN CRYOPLUNGE 3). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 5806 |
| Reported Resolution (Å) | 12 |
| Resolution Method | FSC 0.5 CUT-OFF |
| Other Details | (Single particle details: The particles were selected using semi-automatic program e2boxer.py.) (Single particle--Applied symmetry: I) |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3J6R) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--rigid body | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 15 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2014-07-22 |
| Temperature (Kelvin) | 95 |
| Microscope Model | JEOL 2100 |
| Minimum Defocus (nm) | 1600 |
| Maximum Defocus (nm) | 5430 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN LIQUID NITROGEN |
| Nominal Magnification | 50000 |
| Calibrated Magnification | |
| Source | LAB6 |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Situs | |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | Auto3DEM | |
| RECONSTRUCTION | EMAN | 2 |
| RECONSTRUCTION | RELION | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| each particle | ||||
