ELECTRON MICROSCOPY

Sample

Adeno-associated virus - 2

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details 4ul of AAV-2 (1.7uM) was added to the grid, followed by 4ul of AAVR-PKD1-2 (16.7uM), with manual blotting after each addition with Whatman paper (Cat. no. 1001-110.) 4ul of buffer containing 25mM HEPES, 150mM NaCl, pH 7.4 was added to the grid before final blotting and plunge-freezing in the Vitrobot (blot time 1.5sec, blot force -1).
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 21373
Reported Resolution (Å) 2.4
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Map values at grid points within 2 Angstrom of atoms
Overall B Value ?
Fitting Procedure ?
Details An initial model for AAVR was constructed by homology modeling using Modeller 9.2. After remodeling AAVR and the crystal structure of AAV2, the structure was refined using RSRef embedded in CNS for stereochemically restrained torsion angle simulated annealing and gradient descent optimization. Stand-alone RSRef was used for refinement of EM envelope corrections, resolution estimates, and restrained atomic B-factors.
Data Acquisition
Detector Type FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å2) 25.4
Imaging Experiment
Date of Experiment ?
Temprature (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 FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 75000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 3.0b
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION Gctf 1.06
MODEL FITTING Coot ?
INITIAL EULER ASSIGNMENT RELION 3.0b
FINAL EULER ASSIGNMENT RELION 3.0b
CLASSIFICATION RELION 3.0b
RECONSTRUCTION RELION 3.0b
MODEL REFINEMENT RSRef ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?