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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9J4C
pdb_00009j4c
10.2210/pdb9j4c/pdb
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FASTA
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Binary MMCIF
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Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
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MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Dimer complex of Human Plexin-A1 27-710 with aPlexinA1-19-43 Fab binding
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
To prepare cryo-grids, 3 ul samples were applied to glow discharged Quantifoil Au grids (R2/2, 300 mesh), which were subsequently blotted with filter paper (Ted Pella) for 3 seconds at 18oC and 100% humidity. The grids were immediately plunge frozen in liquid ethane using a FEI Vitrobot IV (ThermoFisher)
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
253734
Reported Resolution (Å)
3.33
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
AB INITIO MODEL
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
Initial local fitting was done using Chimera X, followed by manual fitting using Coot. Finally it was refined using Phenix real space refinement
Data Acquisition
Detector Type
FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å
2
)
50.0
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1200
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
OTHER
Specimen Holder Model
?
Nominal Magnification
?
Calibrated Magnification
?
Source
OTHER
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.1.2
CTF CORRECTION
cryoSPARC
4.1.2
MODEL FITTING
UCSF ChimeraX
?
MODEL FITTING
Coot
0.9.8.7
INITIAL EULER ASSIGNMENT
cryoSPARC
4.1.2
FINAL EULER ASSIGNMENT
cryoSPARC
4.1.2
CLASSIFICATION
cryoSPARC
4.1.2
RECONSTRUCTION
cryoSPARC
4.1.2
MODEL REFINEMENT
PHENIX
1.21
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
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