3J6R
Electron cryo-microscopy of Human Papillomavirus Type 16 capsid
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DZL |
Sample |
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Human Papilloma Virus type 16 capsid |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA KF80 |
Cryogen Name | ETHANE |
Sample Vitrification Details | Plunged into liquid ethane (LEICA KF80) |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 5952 |
Reported Resolution (Å) | 9.1 |
Resolution Method | FSC 0.33 CUT-OFF |
Other Details | (Single particle--Applied symmetry: I) |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1DZL) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | REFINEMENT PROTOCOL--flexible DETAILS--Rigid fitting of domain copies in asymmetric unit, followed by molecular dynamics-based flexible fitting, addi ... |
Data Acquisition | |||||||||
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Detector Type | KODAK SO-163 FILM | ||||||||
Electron Dose (electrons/Å**2) |
Imaging Experiment | 1 |
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Date of Experiment | 2010-02-02 |
Temperature (Kelvin) | |
Microscope Model | FEI/PHILIPS CM200FEG |
Minimum Defocus (nm) | 537 |
Maximum Defocus (nm) | 2175 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN LIQUID NITROGEN |
Nominal Magnification | 38000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 120 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | MDFF | |
MODEL FITTING | NAMD | |
MODEL FITTING | PyMOL | |
MODEL FITTING | UCSF Chimera | |
MODEL FITTING | VMD | |
RECONSTRUCTION | Auto3DEM | |
RECONSTRUCTION | Bsoft |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
each micrograph |