8RH1
Trimeric HSV-2F gB ectodomain in postfusion conformation with three bound HDIT101 Fab molecules.
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GUM |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 33.292 |
r_long_range_B_other | 33.292 |
r_scangle_other | 21.231 |
r_mcangle_it | 17.872 |
r_mcangle_other | 17.871 |
r_dihedral_angle_3_deg | 15.452 |
r_scbond_it | 12.604 |
r_scbond_other | 12.603 |
r_mcbond_it | 10.961 |
r_mcbond_other | 10.961 |
Sample |
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Trimeric HSV-2G gB ectodomain in post-fusion conformation with three bound HDIT101 Fab molecules |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 234096 |
Reported Resolution (Å) | 3.45 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (2gum) | ||||
Refinement Space | |||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 1.325 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS GLACIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | RELION | 4.0 |
IMAGE ACQUISITION | SerialEM | 3.8 |
CTF CORRECTION | CTFFIND | 4.1.14 |
MODEL FITTING | CCP4 package | 1.6 |
INITIAL EULER ASSIGNMENT | RELION | 4.0 |
FINAL EULER ASSIGNMENT | RELION | 4.0 |
CLASSIFICATION | RELION | 4.0 |
RECONSTRUCTION | RELION | 4.0 |
MODEL REFINEMENT | CCP4 package | 1.6 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 6289845 |