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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VHH |
Refinement
RMS Deviations | |
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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 |
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Bacterial nitrilase filament with covalent adduct derived from benzonitrile hydrolysis. |
Specimen Preparation | |
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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 | |
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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 | |||||
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Id | 1 (2VHH) | 2 | |||
Refinement Space | REAL | ||||
Refinement Protocol | BACKBONE TRACE | ||||
Refinement Target | |||||
Overall B Value | 40 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 1 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE | 140381 |