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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
5VN8
pdb_00005vn8
10.2210/pdb5vn8/pdb
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Structure Factors
Full Validation Report
Validation File (XML)
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Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
HIV-1 Env B41 SOSIP.664 in complex with b12 fragment antigen binding
Specimen Preperation
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, followed by immediate plunging
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
88071
Reported Resolution (Å)
3.6
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
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. b12 coordinates taken from PDB 2NY7. Performed fragment based refinement using Rosetta, followed by relaxed refinement in Rosetta. Modeled glycans using Chimera and performed final refinements using Phenix.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å
2
)
58
Imaging Experiment
Date of Experiment
?
Temprature (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
?
Imaging Experiment
Task
Software Package
Version
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
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
