+Open data
-Basic information
Entry | Database: PDB / ID: 6wgb | ||||||
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Title | Crystal structure of the fab portion of dupilumab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Dupilumab / hIL4R | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Druzina, Z. / Atwell, S. / Pustilnik, A. / Antonysamy, S. / Ho, C. / Lieu, R. / Hendle, J. / Benach, J. / Wang, J. | ||||||
Citation | Journal: Plos One / Year: 2020 Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing. Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wgb.cif.gz | 164.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wgb.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wgb_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 6wgb_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 6wgb_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 6wgb_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/6wgb ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wgb | HTTPS FTP |
-Related structure data
Related structure data | 6wg8C 6wgjC 6wgkC 6wglC 6wioC 6wirC C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 25233.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 24042.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100mM Bis-Tris pH 5.5, 25% PEG 3350 , 200mM Magnesium Chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 17, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.99→67.71 Å / Num. obs: 64075 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 12.7 / Num. measured all: 217034 / Scaling rejects: 112 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.2 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: self Resolution: 1.99→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.883 / SU B: 5.779 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.193 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.14 Å2 / Biso mean: 32.495 Å2 / Biso min: 10.74 Å2
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Refinement step | Cycle: final / Resolution: 1.99→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.991→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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