ELECTRON MICROSCOPY

Sample

Adeno-associated virus

Specimen Preperation
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 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
Map-Model Fitting and Refinement
ID 1
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-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/Å2) 30
Imaging Experiment
Date of Experiment ?
Temprature (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.).
Imaging Experiment
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 ?
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