8DTO
Vaccine elicited Antibody MU89 bound to CH848.D949.10.17_N133D_N138T.DS.SOSIP.664 HIV-1 Env trimer
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6UM6 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.142 |
f_angle_d | 0.756 |
f_chiral_restr | 0.053 |
f_bond_d | 0.005 |
f_plane_restr | 0.005 |
Sample |
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V3-glycan vaccine induced antibody MU89 in complex with CH848.3.D0949.10.17chim.6R.DS.SOSIP.664_N133D_N138T HIV Env trimer |
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 | 72478 |
Reported Resolution (Å) | 3.57 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (6UM6) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 58.9 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 700 |
Maximum Defocus (nm) | 2500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | |
IMAGE ACQUISITION | Latitude | |
CTF CORRECTION | cryoSPARC | 3.2 |
MODEL FITTING | UCSF ChimeraX | |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.2 |
CLASSIFICATION | cryoSPARC | 3.2 |
RECONSTRUCTION | cryoSPARC | 3.2 |
MODEL REFINEMENT | PHENIX | |
MODEL REFINEMENT | Coot | |
MODEL REFINEMENT | ISOLDE |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE | 990218 |