ELECTRON MICROSCOPY

Sample

AlbAB cyclodipeptide oxidase enzyme filament

Specimen Preperation
Sample Aggregation State FILAMENT
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Grid was plunge frozen into liquid ethane using the following parameters: blot force- 5, blot time 2 seconds
3D Reconstruction
Reconstruction Method HELICAL
Number of Particles 795765
Reported Resolution (Å) 2.78
Resolution Method FSC 0.143 CUT-OFF
Other Details Final reconstruction was generated by a masked local refinement of the helically refined map. The mask encompassed one dimer of AlbA and two surrounding dimers of AlbB.
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Cross-correlation coefficient
Overall B Value 107.4
Fitting Procedure ?
Details A model of AlbAB was created using AlphaFold2 using MMseqs2 via ColabFold. The model was then fit into the cryoEM density using ChimeraX. The model was then iteratively refined using Coot v 0.9.8.1 and real-space refinement in Phenix v 1.20.1-4487.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 50.12
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 2500
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 105000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.2.1
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION cryoSPARC 4.2.1
MODEL FITTING UCSF ChimeraX 1.5
INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1
RECONSTRUCTION cryoSPARC 4.2.1
MODEL REFINEMENT PHENIX 1.20.1-4487
MODEL REFINEMENT Coot 0.9.8.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?