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Protein Name
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Ligands & Environment
3JBH
?
?
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ELECTRON MICROSCOPY
Sample
Myosin filaments from Tarantula striated muscle
Specimen Preperation
Sample Aggregation State
FILAMENT
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
Blotting was performed from one side of the grid till a thin sample film on it using Whatman No 42 filter paper, then the grid was immediately plunged under gravity into liquid ethane cooled by liquid nitrogen. Grids were stored under liquid nitrogen.
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
?
Reported Resolution (Å)
20
Resolution Method
FSC 0.5 CUT-OFF
Other Details
Three-dimensional single particle reconstruction was carried out by a modification of the IHRSR method, using SPIDER. Low-dose electron micrographs of 1008 frozen-hydrated thick filaments halves ere digitized at 0.248 nm per pixel using a Nikon Super Coolscan 8000 ED scanner. Filaments were aligned with the bare zone at the top, to ensure correct polarity in subsequent steps. A total of 15,504 segments, each 62 nm long, with an overlap of 55.8 nm, and containing aprox. 40,000 unique pairs of interacting myosin heads went into the reconstruction. As an initial reference model we used the tarantula negatively stained 3D-map, which was axially rotated, axially shifted and also out of plane tilted up to plus-minus12deg. for projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus12deg. every 2deg., 45 reference rotated projections (0-90 degrees, 2deg. rotation angle), and 7 image axial shifts of 2.2 nm. The resulting 3D-map combines about 10,700 out of 15,504 filament segments, a yield of 69 percent of included segments. There are 4 helices of myosin heads, rotated 30 degrees, every 145 Angstroms. The filament segments were selected based on visual judgement of good helical order.
Refinement Type
Symmetry Type
HELICAL
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Correlation
Overall B Value
?
Fitting Procedure
?
Details
METHOD--FLEXIBLE FITTING DETAILS--Protocol- Flexible Fitting. The flexible docking procedure is based on a connected (motion capture) network of identified features within the atomic model. The atomic model is allowed to move according to displacements tracked by 31 control points defined by the network, in order to find the best match to the cryo-EM map
Data Acquisition
Detector Type
KODAK SO-163 FILM
Electron Dose (electrons/Å
2
)
.
Imaging Experiment
Date of Experiment
2002-10-23
Temprature (Kelvin)
Microscope Model
FEI/PHILIPS CM120T
Minimum Defocus (nm)
1950
Maximum Defocus (nm)
1950
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.0
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
35000
Calibrated Magnification
35000
Source
LAB6
Acceleration Voltage (kV)
120
Imaging Details
low dose
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
Situs
2.3
RECONSTRUCTION
SPIDER
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
