3JBI

MDFF model of the vinculin tail domain bound to F-actin

ELECTRON MICROSCOPY

Sample
Vinculin tail domain bound to F-actin
Sample Components
skeletal muscle actin
Vinculin tail domain, residues 879-1061

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar Vt was then ...	3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar Vt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of Vt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging into liquid ethane (LEICA EM GP).

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles
Reported Resolution (Å)	8.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details	(Helical Details: Single model IHRSR was performed with EMAN2 / SPARX and final reconstruction with FREALIGN (fixed helical parameters).)
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	27.8
Angular Rotation	166.82

Map-Model Fitting and Refinement
Id	1 (1QKR)	2 (3J8A)
Refinement Space	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible DETAILS--Components were initially rigid body fit using Chimera, followed by flexible fitting with MDFF.	REFINEMENT PROTOCOL--flexible DETAILS--Components were initially rigid body fit using Chimera, followed by flexible fitting with MDFF.

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2014-05-22
Temperature (Kelvin)
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	100000
Calibrated Magnification	137615
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	CTFFIND	3
MODEL FITTING	MDFF
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	SPARX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	FREALIGN (per segment)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.