6I1Y
Vibrio vulnificus EpsD
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5WQ8 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 76.575 |
| r_long_range_B_other | 76.575 |
| r_scangle_other | 67.24 |
| r_scbond_other | 43.059 |
| r_scbond_it | 43.058 |
| r_mcangle_it | 38.684 |
| r_mcangle_other | 38.684 |
| r_dihedral_angle_2_deg | 27.407 |
| r_mcbond_other | 26.257 |
| r_mcbond_it | 26.256 |
| Sample |
|---|
| EpsD |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 46126 |
| Reported Resolution (Å) | 3.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C15 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5WQ8) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 146 | ||||
| Fitting Procedure | |||||
| Details | Coot and buccaneer for model building and refmac5 for refinement (CCPEM-1.1.0 suite). | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN LIQUID NITROGEN |
| Nominal Magnification | |
| Calibrated Magnification | 41322 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Latitude | S |
| CTF CORRECTION | Gctf | |
| CTF CORRECTION | RELION | 2.1 |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | RELION | 2.1 |
| FINAL EULER ASSIGNMENT | RELION | 2.1 |
| CLASSIFICATION | RELION | 2.1 |
| RECONSTRUCTION | RELION | 2.1 |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 125884 | |||
