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PDB Id
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Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3J5Q
pdb_00003j5q
10.2210/pdb3j5q/pdb
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Structure Factors
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Validation File (XML)
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Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Rat TRPV1 in complex with DkTx and resiniferatoxin
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE
Sample Vitrification Details
Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
36158
Reported Resolution (Å)
3.8
Resolution Method
FSC 0.143 CUT-OFF
Other Details
The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density. Interatomic clashes between the ankyrin repeats and the C-terminal beta sheet are the result of poor geometry due to relatively poor experimental density in these regions. Resolution and averaging of DkTx density was insufficient to provide side chain geometry. The DkTx model was generated as a poly-ALA model based on hanatoxin (PDB entry 1D1H) and docked into the DkTx density with slight modification. (Single particle details: 3D classification, refinement, and reconstruction were performed using RELION) (Single particle--Applied symmetry: C4)
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
REFINEMENT PROTOCOL--de novo model building DETAILS--The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å
2
)
21
Imaging Experiment
Date of Experiment
2013-01-01
Temprature (Kelvin)
Microscope Model
FEI POLARA 300
Minimum Defocus (nm)
1500
Maximum Defocus (nm)
3000
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.0
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
OTHER
Nominal Magnification
31000
Calibrated Magnification
31000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Gatan K2 Summit operated in super-resolution counting mode, image recorded with dose fractionation method.
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
Each particle
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