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Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3J8W
?
?
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FASTA
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ELECTRON MICROSCOPY
Sample
quasi-HPV16 complexed with H263.A2 Fabs
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
GATAN CRYOPLUNGE 3
Cryogen Name
ETHANE
Sample Vitrification Details
Plunged into liquid ethane (GATAN CRYOPLUNGE 3).
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
8908
Reported Resolution (Å)
13.0
Resolution Method
FSC 0.5 CUT-OFF
Other Details
Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values used to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstruction was initiated using a random model generated with setup_rmc and reached 14 A resolution estimated at a Fourier Shell Correlation (FSC) of 0.5. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2. (Single particle details: The particles were selected using semi-automatic program e2boxer.py (EMAN2)) (Single particle--Applied symmetry: I)
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
REFINEMENT PROTOCOL--RIGID BODY
Data Acquisition
Detector Type
GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å
2
)
15
Imaging Experiment
Date of Experiment
2014-07-31
Temprature (Kelvin)
Microscope Model
JEOL 2100
Minimum Defocus (nm)
1490
Maximum Defocus (nm)
5520
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
GATAN LIQUID NITROGEN
Nominal Magnification
40000
Calibrated Magnification
?
Source
LAB6
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
Situs
?
MODEL FITTING
UCSF Chimera
?
RECONSTRUCTION
Auto3DEM
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
Each particle
