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 7KP3 | pdb_00007kp3

Adeno-associated virus serotype 5 at 2.1 Angstroms resolution, AAV5


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NTT 
Sample
Adeno-associated virus
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsTwo 2uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles373426
Reported Resolution (Å)2.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (3NTT)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetLeast-squares residual
Overall B Value
Fitting Procedure
DetailsStand-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 TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)31.7
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)-700
Maximum Defocus (nm)-2700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsComa-free alignment and objective astigmatism where corrected using Sherpa (Thermo Fisher, Inc.).
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1 beta
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4
MODEL FITTINGCoot0.8.9.2
INITIAL EULER ASSIGNMENTRELION3.1 beta
FINAL EULER ASSIGNMENTRELION3.1 beta
CLASSIFICATIONRELION3.1 beta
RECONSTRUCTIONRELION3.1 Beta
MODEL REFINEMENTRSRef0.5.8
MODEL REFINEMENTCNS1.3
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLYCTF correction was performed on a per particle basis.672106LoG Picker was used for initial automated particle selection. Templates were then generated by 2D classification, followed by particle template selection in Relion 3.1 beta.