+Open data
-Basic information
Entry | Database: PDB / ID: 5ilt | ||||||
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Title | Crystal structure of bovine Fab A01 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody fab ultralong CDR H3 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Stanfield, R.L. / Wilson, I.A. | ||||||
Citation | Journal: Sci Immunol / Year: 2016 Title: Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies. Authors: Stanfield, R.L. / Wilson, I.A. / Smider, V.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ilt.cif.gz | 272.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ilt.ent.gz | 225.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ilt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ilt_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 5ilt_full_validation.pdf.gz | 428.5 KB | Display | |
Data in XML | 5ilt_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 5ilt_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/5ilt ftp://data.pdbj.org/pub/pdb/validation_reports/il/5ilt | HTTPS FTP |
-Related structure data
Related structure data | 5e99C 5ihuC 5ijvC 4k3dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 22548.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): 293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 28862.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): 293F / Production host: Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 20% PEG 6000 0.1M bicine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.422 Å / Num. obs: 31935 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 40.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 1.8 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4k3d Resolution: 2→38.422 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.422 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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