2DFS | pdb_00002dfs

3-D structure of Myosin-V inhibited state

ELECTRON CRYSTALLOGRAPHY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W7I
experimental model	PDB	1N2D

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 653	α = 90
b = 653	β = 90
c = 200	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron						M	SINGLE WAVELENGTH

Refinement

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29614
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Sample
Myosin-V

Specimen Preparation
Sample Aggregation State	TISSUE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	liquid ethane

3D Reconstruction
Reconstruction Method	TOMOGRAPHY
Number of Particles	4029
Reported Resolution (Å)	24
Resolution Method
Other Details	Tilt series images were aligned using marker-free alignment. Molecular volumes extracted from the cryotomograms, aligned in 3-D. Marker-free alignment is described in the reference: Winkler,H. and Taylor,K.A. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy, 106, 240-254 (2006)
Refinement Type
Symmetry Type	2D CRYSTAL

Map-Model Fitting and Refinement
Id	1 (1W7I, 1N2D)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross correlation
Overall B Value
Fitting Procedure
Details	METHOD--Rigid body docking first and then refined with normal mode flexible fitting. REFINEMENT PROTOCOL--Rigid body docking and normal mode flexible fitting. For the fitting the density corresponding to the two myosin V heads within the asymmetric unit was segmented from the rest of the map using the watershed transform (Volkman 2002. J.STRUCT.BIOL. 138, 123-129). After fitting the atomic model against the head density, the coordinates were not refined further against the nearest neighbor myosin V heads to remove bad crystal contacts. The alpha-helical coiled-coil domain was manually fit to the and not refined further.

Data Acquisition
Detector Type	TVIPS TEMCAM-F224 (2k x 2k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment	2004-02-01
Temperature (Kelvin)	103
Microscope Model	FEI/PHILIPS CM300FEG/ST
Minimum Defocus (nm)	12000
Maximum Defocus (nm)	4000
Minimum Tilt Angle (degrees)	-70
Maximum Tilt Angle (degrees)	70
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	24000
Calibrated Magnification	24000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	NMFF
MODEL FITTING	Situs
RECONSTRUCTION	PROTOMO

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTF gradient correction