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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3J7E
pdb_00003j7e
10.2210/pdb3j7e/pdb
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FASTA
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Binary MMCIF
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Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
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Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
GATAN CRYOPLUNGE 3
Cryogen Name
ETHANE
Sample Vitrification Details
Blot for 0.7 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
2075
Reported Resolution (Å)
13.6
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 to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstructions were 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--Applied symmetry: I)
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
REFINEMENT PROTOCOL--flexible
Data Acquisition
Detector Type
GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å
2
)
15
Imaging Experiment
Date of Experiment
2013-10-30
Temprature (Kelvin)
Microscope Model
JEOL 2100
Minimum Defocus (nm)
690
Maximum Defocus (nm)
3990
Minimum Tilt Angle (degrees)
0.0
Maximum Tilt Angle (degrees)
0.0
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
GATAN LIQUID NITROGEN
Nominal Magnification
80000
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
?
RECONSTRUCTION
EMAN
2
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
Each particle
