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PDB Id
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Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3DTP
pdb_00003dtp
10.2210/pdb3dtp/pdb
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ELECTRON MICROSCOPY
Sample
Myosin thick filaments from Tarantula striated muscle
Specimen Preperation
Sample Aggregation State
FILAMENT
Vitrification Instrument
?
Cryogen Name
?
Sample Vitrification Details
Plunging in a liquid ethane. 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
15504
Reported Resolution (Å)
20
Resolution Method
?
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 were 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-minus 12 deg. every 2 deg., 45 reference rotated projections (0-90 deg., every 2 deg. 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.
Refinement Type
Symmetry Type
HELICAL
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Constrained Molecular Dynamics
Overall B Value
?
Fitting Procedure
?
Details
METHOD--Flexible Fitting REFINEMENT PROTOCOL--Custom skeleton of 31 positional markers
Data Acquisition
Detector Type
.
Electron Dose (electrons/Å
2
)
.
Imaging Experiment
Date of Experiment
2001-09-19
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
Holey carbon grids Cryo preserved in Liquid ethane were observed in a Philips CM120 electron microscope under low dose conditions. Only filaments on thin carbon over holes were photographed
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
Situs
3.2
MODEL FITTING
X-PLOR
3.851
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
no corrected
