7KFR

Adeno-Associated Virus (AAV-DJ) - cryo-EM structure at 1.56 Angstrom Resolution

ELECTRON MICROSCOPY

Sample
Adeno-associated virus

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Two 3uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	48209
Reported Resolution (Å)	1.56
Resolution Method	FSC 0.143 CUT-OFF
Other Details	These 48209 particles refined to approx. 2.2 A with I1 symmetry, and subsequent refinements of beam tilt and per-particle CTF brought the resolution t ...	These 48209 particles refined to approx. 2.2 A with I1 symmetry, and subsequent refinements of beam tilt and per-particle CTF brought the resolution to 1.8 A. Further particle-polishing and subsequent re-refinement of CTF brought the resolution to 1.70 A and a final reconstruction using Ewald sphere correction ended at 1.56 A. The map used for modeling was sharpened using the volume whitening routine in cisTEM.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (5UF6)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Least-squares residual
Overall B Value
Fitting Procedure
Details	Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embed ...	Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embedded CNS was used for molecular dynamics optimization (1st round) and stereochemically-restrained all-atom least-squares optimization.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	-800
Maximum Defocus (nm)	-2600
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	155000
Calibrated Magnification	154400
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Coma-free alignment and objective astigmatism where corrected using Sherpa (Thermo Fisher, Inc.).

EM Software
Task	Software Package	Version
PARTICLE SELECTION	DoG Picker
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
MODEL FITTING	Coot	0.8.9.2
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.0
CLASSIFICATION	RELION	3.0
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	RSRef	0.5.8
MODEL REFINEMENT	CNS	1.3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY		75316	DoG (Difference of Gaussian) Picker was used for initial automated particle selection. Templates were then generated by 2D classification, followed by particle template selection in Relion 3.0.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.