8UXU
Cryo-EM structure of a bacterial nitrilase filament with a covalent adduct derived from benzonitrile hydrolysis
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2VHH | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.1569 |
| f_angle_d | 0.5366 |
| f_chiral_restr | 0.0462 |
| f_bond_d | 0.0063 |
| f_plane_restr | 0.0043 |
| Sample |
|---|
| Bacterial nitrilase filament with covalent adduct derived from benzonitrile hydrolysis. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grids were glow-discharged for 60 sec before deposition of 3 ul sample, blotted for 4 s, and vitrified by plunging into liquid ethane and stored in a ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 56369 |
| Reported Resolution (Å) | 3.01 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | D1 |
| Axial Rise | 18.2573 |
| Angular Rotation | -72 |
| Axial Symmetry | D1 |
| Axial Rise | 18.2573 |
| Angular Rotation | -72 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2VHH) | 2 | |||
| Refinement Space | REAL | ||||
| Refinement Protocol | BACKBONE TRACE | ||||
| Refinement Target | |||||
| Overall B Value | 40 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 5000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 75000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.0.8 |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | Coot | 0.9.8.7 |
| MODEL REFINEMENT | REFMAC | 5 |
| MODEL FITTING | Coot | 0.9.8.7 |
| MODEL FITTING | ISOLDE | |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0.8 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.8 |
| RECONSTRUCTION | RELION | 3.0.8 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 140381 | |||
