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Open data
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Basic information
Entry | Database: PDB / ID: 6x5e | ||||||
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Title | Crystal structure of a Lewis-binding Fab (ch88.2) | ||||||
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![]() | IMMUNE SYSTEM / immunoglobulin / chimeric antibody / antigen binding fragment / Lewis-binding antibody | ||||||
Function / homology | NICKEL (II) ION![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Soliman, C. / Ramsland, P.A. | ||||||
![]() | ![]() Title: Molecular and structural basis for Lewis glycan recognition by a cancer-targeting antibody. Authors: Soliman, C. / Guy, A.J. / Chua, J.X. / Vankemmelbeke, M. / McIntosh, R.S. / Eastwood, S. / Truong, V.K. / Elbourne, A. / Spendlove, I. / Durrant, L.G. / Ramsland, P.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 392.3 KB | Display | ![]() |
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PDB format | ![]() | 261.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.1 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 43.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4x80S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23644.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 24431.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG MME 200, Tris, Nickel (II) chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. obs: 44428 / % possible obs: 92.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 60.41 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.07 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.29→2.4 Å / Num. unique obs: 6787 / CC1/2: 0.719 / Rrim(I) all: 0.88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4X80 Resolution: 2.29→33.49 Å / SU ML: 0.4361 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 37.6612 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→33.49 Å
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Refine LS restraints |
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LS refinement shell |
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