Structure of the Neisseria gonorrhoeae Type IV pilus filament from x-ray crystallography and electron cryomicroscopy
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2HI2 | |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| The GC pilus filament structure was built by computationally fitting a single GC pilin subunit (2HI2.pdb) into a cryoEM density map of the pilus filament (EMDB code xxx) using the program CoAn (Volkmann and Hanein, J. Struct. Biol., 125, 176-184, 1999), and then applying the symmetry operators defined by the cryoEM reconstruction (10.5 Angstrom rise and a 100.8 degree azimuthal rotation, Craig et al., Mol. Cell xxx, yyy, 2006) to the subunit. | CoAn | |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CoAn | ||
| Sample |
|---|
| N. gonorrhoeae Type IV pili |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 5 ul of sample were applied to grids for 1 minute, blotted for 2.5 seconds then plunge-frozen in liquid ethane using an FEI Vitrobot |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 25000 |
| Reported Resolution (Å) | 12.5 |
| Resolution Method | |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2HI2) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | real-space density correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--CoAn REFINEMENT PROTOCOL--rigid body | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 10 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2004-06-23 |
| Temperature (Kelvin) | 95 |
| Microscope Model | FEI/PHILIPS CM200FEG |
| Minimum Defocus (nm) | 1100 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 50000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 120 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | CoAn | |
| RECONSTRUCTION | IHRSR | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| Wiener filter | ||||
