8PB9
Cryo-EM structure of the c-di-GMP-bound FleQ-FleN master regulator complex from Pseudomonas aeruginosa
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.641 |
| f_angle_d | 0.824 |
| f_chiral_restr | 0.043 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.005 |
| Sample |
|---|
| C-di-GMP bound FleQ-FleN complex from Pseudomonas aeruginosa |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | triple deposition |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 1283732 |
| Reported Resolution (Å) | 3.3 |
| Resolution Method | OTHER |
| Other Details | Due to flexibility, preferential orientation and partial occupancy for one of the subunits, the data was downsampled and the resolution used for refin ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | 2 | 3 | ||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Crystal structures fitting Refined in Phenix, coot and Namdinator | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.3 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | PHENIX | |
| MODEL FITTING | UCSF ChimeraX | |
| CLASSIFICATION | cryoSPARC | |
| RECONSTRUCTION | cryoSPARC | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Gctf through cryoSPARC interface | |||
