5VN3
Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.354 |
f_angle_d | 1.177 |
f_chiral_restr | 0.06 |
f_bond_d | 0.009 |
f_plane_restr | 0.008 |
Sample |
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HIV-1 Env B41 SOSIP.664 in complex with soluble CD4 (2-domain) and 17b fragment antigen binding |
Sample Components |
HIV-1 Env B41 SOSIP.664 |
CD4 (2-domain) |
17b fragment antigen |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, follo ... |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 46855 |
Reported Resolution (Å) | 3.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C3 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | EMRinger | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Homology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. sCD4 and 17b coordinates taken from PDB 1GC1. Performed fragment based refine ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 58 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 4000 |
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 | 22500 |
Calibrated Magnification | 38168 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | DoG Picker | |
IMAGE ACQUISITION | Leginon | |
CTF CORRECTION | Gctf | 1.06 |
MODEL FITTING | UCSF Chimera | 1.10.1 |
MODEL REFINEMENT | Rosetta | 2016.02.58402 |
MODEL REFINEMENT | PHENIX | 1.11.1-2575 |
INITIAL EULER ASSIGNMENT | RELION | 2.0 |
FINAL EULER ASSIGNMENT | RELION | 2.0 |
CLASSIFICATION | RELION | 2.0 |
RECONSTRUCTION | RELION | 2.0 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |