6RWK
MxiD N0 N1 and MxiG C-terminal domains of the Shigella type 3 secretion system
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.157 |
| f_angle_d | 0.744 |
| f_chiral_restr | 0.046 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.005 |
| Sample |
|---|
| Oligomer of the secretin N0 and N1 domains in complex with the inner membrane ring of the Shigella type 3 secretion system |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Dra ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 72298 |
| Reported Resolution (Å) | 3.86 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C8 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3GR5) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | Correlation coefficient and geometry | ||||
| Overall B Value | 120 | ||||
| Fitting Procedure | |||||
| Details | Model was built and refined in the map low-pass filtered at 3.5 A | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 25 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1.5 |
| Maximum Defocus (nm) | 4 |
| 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 | 101179 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 1.4 |
| CTF CORRECTION | CTFFIND | 3.5 |
| MODEL FITTING | UCSF Chimera | 1.13.1 |
| INITIAL EULER ASSIGNMENT | RELION | 2.1 |
| FINAL EULER ASSIGNMENT | RELION | 2.1 |
| CLASSIFICATION | RELION | 2.1 |
| RECONSTRUCTION | RELION | 2.1 |
| MODEL REFINEMENT | PHENIX | 3357 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 171833 | |||
