6TIK
Hepatitis B virus core shell--virus-like particle with NadA epitope
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.539 |
f_angle_d | 0.8561 |
f_chiral_restr | 0.0517 |
f_bond_d | 0.008 |
f_plane_restr | 0.0066 |
Sample |
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VLP fusion sequence expressed in E.coli. |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 ul applied for 30s at room temperature, then 4 - 5 s blot |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 8598 |
Reported Resolution (Å) | 3.4 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1QGT) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Correlation with the map plus geometry | ||||
Overall B Value | 111.33 | ||||
Fitting Procedure | |||||
Details | The 4 protein chains from the original T=4 HBV core shell structure solved by X-ray crystallography (Wynne, Leslie, Crowther, 1999), PDB code 1QGT, re ... |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 79 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 104167 |
Calibrated Magnification | 100719 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | EMAN2 | 2.01 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | EMAN2 | 2.01 |
MODEL FITTING | DockEM | |
MODEL REFINEMENT | PHENIX | PHENIX.real-space_refine |
INITIAL EULER ASSIGNMENT | cryoSPARC | v0.65 |
FINAL EULER ASSIGNMENT | cryoSPARC | v0.65 |
CLASSIFICATION | cryoSPARC | v0.65 |
RECONSTRUCTION | cryoSPARC | v0.65 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 10119 | Initially ~44,000 particles were initially picked and extracted in EMAN. Approx 12,000 were shell fragments or incomplete. Others were intact but lower resolution, so damaged or affected by charging, or other issue. After filtering/cleaning by EMAN2 2D classification 10119 particles were taken forwards for initial 3D reconstruction in EMAN2. This set of 10119 was then 2D cleaned by CryoSPARC to give 9145 particles. |