Skip to main content

 6E9D | pdb_00006e9d

Sub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM Reconstruction of AAV-2 L336C


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LP3 
Sample
Adeno-associated virus - 2
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsDouble blotting was used to increase particle concentration. Sample was added to a plasma-cleaned (Gatan Solarus) grid and blotted away using Whatman ...Double blotting was used to increase particle concentration. Sample was added to a plasma-cleaned (Gatan Solarus) grid and blotted away using Whatman grade 4 filter paper after 20 second wait time.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles30515
Reported Resolution (Å)1.86
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsFrequency limited refinement
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (1LP3)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient, EM ringer score
Overall B Value61.9
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)22.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)600
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification37000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsBeam tilt in 8 directions +/- 5 mrad
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatch0.56
IMAGE ACQUISITIONLeginon
CTF CORRECTIONRELION2.1
MODEL FITTINGCoot0.8.9.1
MODEL REFINEMENTPHENIX1.13
INITIAL EULER ASSIGNMENTcryoSPARC0.65
FINAL EULER ASSIGNMENTFREALIGN9.11
CLASSIFICATIONFREALIGN9.11
RECONSTRUCTIONFREALIGN9.11
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF estimation per particle - Gctf, CTF estimation per micrograph - CTFFIND478194Template-based picking by generating template from a 2-D classification of an initial subset of data.