Home
About
Browse
Covid-19
Organism Classification
Alphafold Collection
Virus Classification
Indian Data
Documentation
Contact
Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3JAX
pdb_00003jax
10.2210/pdb3jax/pdb
Download file
FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Myosin thick filaments from Schistosoma mansoni smooth muscle
Specimen Preperation
Sample Aggregation State
FILAMENT
Vitrification Instrument
Cryogen Name
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
9500
Reported Resolution (Å)
23.0
Resolution Method
FSC 0.5 CUT-OFF
Other Details
For each iteration of reconstruction (30 cycles), filament segment projections were compared with different projections of the reference reconstruction as follows: seven 2.3 nm axial shifts, 2 degree intervals of rotation about the filament axis up to 90 degrees, and 2 degree intervals of out-of-plane tilting from -10 degrees to +10 degrees. The total number of projections was 7 x 45 x 11 = 3465. For the final 19 cycles of the reconstruction, we used only the best-ordered 420 filament halves (those in which >30% of the segments were found good enough to be used by the reconstruction script in the back-projection in previous cycles). From ~17,000 segments, ~9,500 (56%) were included in the final reconstruction. This final 3D-reconstruction was the average of the last 19 reconstructions between cycles 12 - 30. Its resolution, according to the 0.5 Fourier Shell Correlation (FSC) criterion, was 2.3 nm.
Refinement Type
Symmetry Type
HELICAL
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
METHOD--rigid docking REFINEMENT PROTOCOL--RIGID BODY DETAILS--3DTP was fitted as a rigid body using the Fit in Map tool of UCSF Chimera.
Data Acquisition
Detector Type
TVIPS TEMCAM-F224 (2k x 2k)
Electron Dose (electrons/Å
2
)
10
Imaging Experiment
Date of Experiment
2013-02-15
Temprature (Kelvin)
Microscope Model
FEI/PHILIPS CM120T
Minimum Defocus (nm)
600
Maximum Defocus (nm)
2400
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.0
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
SIDE ENTRY, EUCENTRIC
Nominal Magnification
42000
Calibrated Magnification
42000
Source
LAB6
Acceleration Voltage (kV)
80
Imaging Details
1.5 post-magnification, low-dose conditions
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
UCSF Chimera
?
RECONSTRUCTION
EMAN
2
RECONSTRUCTION
SPIDER
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
Feedback
Feedback Form
Name
Email
Institute
Feedback
Submit
