6NZ0
Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2
ELECTRON MICROSCOPY
Sample |
---|
Adeno-associated virus - 2 |
Sample Components |
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. ... |
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 ... |
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 |