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Binary complex of AAV-2 with a fragment of its cellular receptor, AAVR or dyslexia-associated protein KIAA0319-like protein.
Specimen Preparation
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. ...
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
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1 (1LP3)
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 struc ...
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/Å**2)
25.4
Imaging Experiment
1
Date of Experiment
Temperature (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
EM Software
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
34450
RELION Autopicker using 3D AAV-2 reference filtered to 20A with 15 degree sampling