ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1DZL | |
| Sample |
|---|
| Human Papilloma Virus type 16 capsid |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA KF80 |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Plunged into liquid ethane (LEICA KF80) |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 5952 |
| Reported Resolution (Å) | 9.1 |
| Resolution Method | FSC 0.33 CUT-OFF |
| Other Details | (Single particle--Applied symmetry: I) |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1DZL) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--flexible DETAILS--Rigid fitting of domain copies in asymmetric unit, followed by molecular dynamics-based flexible fitting, addi ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | |||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2010-02-02 |
| Temperature (Kelvin) | |
| Microscope Model | FEI/PHILIPS CM200FEG |
| Minimum Defocus (nm) | 537 |
| Maximum Defocus (nm) | 2175 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN LIQUID NITROGEN |
| Nominal Magnification | 38000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 120 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | MDFF | |
| MODEL FITTING | NAMD | |
| MODEL FITTING | PyMOL | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | VMD | |
| RECONSTRUCTION | Auto3DEM | |
| RECONSTRUCTION | Bsoft | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| each micrograph | ||||
