Experiment: 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 ...	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 cryobox in liquid nitrogen.

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