9RQT | pdb_00009rqt

Heptameric AAV2 Rep40-dsDNA (ITR) complex in presence of ATPgS

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Sample
AAV2 Heptameric Rep40-dsDNA (ITR) in presence of ATPgS

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	137594
Reported Resolution (Å)	2.88
Resolution Method	FSC 0.5 CUT-OFF
Other Details	Composite map generated in phenix using 2 local maps (3-mer local map and 4-mer local map).
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	39.99

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.4.1
IMAGE ACQUISITION	EPU	3.8.1
CTF CORRECTION	cryoSPARC	4.4.1
MODEL FITTING	ISOLDE	1.8
MODEL REFINEMENT	PHENIX	1.21.2_5419
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1
RECONSTRUCTION	cryoSPARC	4.4.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION