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PDB Id
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Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
1O1D
pdb_00001o1d
10.2210/pdb1o1d/pdb
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Validation File (XML)
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Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
INSECT FLIGHT MUSCLE OF THE LARGE WATER BUG LETHOCERUS MAXIMUS
Specimen Preperation
Sample Aggregation State
TISSUE
Vitrification Instrument
?
Cryogen Name
?
Sample Vitrification Details
NO VITRIFICATION. SAMPLES WERE VIEWED AT ROOM TEMPERATURE.
3D Reconstruction
Reconstruction Method
TOMOGRAPHY
Number of Particles
?
Reported Resolution (Å)
70.000
Resolution Method
?
Other Details
3-D MOTIFS WERE IDENTIFIED IN THE TOMOGRAM BY FIRST PRODUCING A CROSS CORRELATION MAP FROM WHICH PEAK COORDINATES WERE DETERMINED FROM THEIR CENTER OF GRAVITY. WE DEFINE A 3-D MOTIF AS ONE, ENTIRE 38.7 NM CROSSBRIDGE REPEAT ALONG ACTIN. THESE MOTIFS USUALLY CONTAIN AT LEAST FOUR MYOSIN HEADS IN TWO PAIRED CROSSBRIDGES (SINGLE CHEVRONS) AND SOMETIMES CONTAIN AS MANY AS SIX MYOSIN HEADS IN FOUR PAIRED CROSSBRIDGES (DOUBLE CHEVRONS). THE REFERENCE FOR THE ANALYSIS WAS SELECTED TO BE CENTERED BETWEEN SUCCESSIVE TROPONIN DENSITIES WHICH COULD BE IDENTIFIED FROM THE IN-PLANE PROJECTION. THE INDIVIDUAL CROSSBRIDGE MOTIFS WERE THEN SUBJECTED TO MULTIVARIATE STATISTICAL ANALYSIS TO IDENTIFY CLUSTERS OF MOTIFS SHOWING SIMILAR CROSSBRIDGE STRUCTURE. THESE CLUSTERS FORMED THE CLASS AVERAGES. THE CHOICE OF STRUCTURE TO BE CLASSIFIED WAS DECIDED BY THE RESOLUTION AND THE LATER PROCESS OF MODEL BUILDING. AVERAGING WAS DONE ACCORDING TO THE HEIRARCHICAL ASCENDENT METHOD. THE RESOLUTION IN EACH OF THE CLASS AVERAGES WAS 7 NM BY THE SPECTRAL SIGNAL TO NOISE RATIO.
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
BEST CORRELATION COEFFICIENT AND FEWEST POOR CONTACTS
Overall B Value
?
Fitting Procedure
?
Details
METHOD--INITIAL MODELS WERE FIT BY HAND USING O. THE FIT WAS THEN REFINED USING REAL SPACE REFINEMENT. REFINEMENT PROTOCOL--RIGID BODY
Data Acquisition
Detector Type
KODAK SO-163 FILM
Electron Dose (electrons/Å
2
)
.
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI/PHILIPS EM400
Minimum Defocus (nm)
?
Maximum Defocus (nm)
?
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
17000
Calibrated Magnification
?
Source
TUNGSTEN HAIRPIN
Acceleration Voltage (kV)
100
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
RSRef
?
RECONSTRUCTION
Custom
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
