3J1S | pdb_00003j1s

Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LP3

Sample
Adeno-associated virus-2 in complex with monoclonal antibody A20
Sample Components
Antibody Fab' fragment
Antibody Fab' fragment
Viral protein

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 2.0 seconds before plunging into liquid ethane (FEI Vitrobot Mark IV).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	11898
Reported Resolution (Å)	8.5
Resolution Method	FSC 0.5 CUT-OFF
Other Details	A20 FAB' WAS MODELED AS THE COMBINATION OF A HOMOLOGY MODEL AND SEQUENCE SEGMENTS EXCERPTED FROM PDB ENTRY 1OSP (SEE REMARK 999 FOR DETAILS). THE AUTHORS STATE THAT ANY INCORRECT PEPTIDE BOND LENGTHS IN THIS ENTRY ARE THE RESULT OF RIGID-BODY FITTING TO A LOW-RESOLUTION MAP OR ARE INHERITED DIRECTLY FROM PDB ENTRY 1OSP.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1LP3)	2	3
Refinement Space	REAL	REAL	REAL
Refinement Protocol	RIGID BODY FIT	RIGID BODY FIT	RIGID BODY FIT
Refinement Target	Least-squares difference between experimental & model coulombic potential	Least-squares difference between experimental & model coulombic potential	Least-squares difference between experimental & model coulombic potential
Overall B Value
Fitting Procedure
Details	METHOD--Rigid Body REFINEMENT PROTOCOL--Rigid Body DETAILS--Anti-bumping restraints from CNS, Constrained icosahedral symmetry	METHOD--Rigid Body REFINEMENT PROTOCOL--Rigid Body DETAILS--Anti-bumping restraints from CNS, Constrained icosahedral symmetry	METHOD--Superimposed according to icosahedral symmetry REFINEMENT PROTOCOL--Fixed DETAILS--Anti-bumping restraints from CNS included 1LP3, Constrained icosahedral symmetry

Data Acquisition
Detector Type	GENERIC GATAN
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2011-02-23
Temperature (Kelvin)	93
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	-500
Maximum Defocus (nm)	-4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	37000
Calibrated Magnification	39775
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	ACE
MODEL FITTING	RSRef
RECONSTRUCTION	Appion
RECONSTRUCTION	EMAN

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Whole image