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Yorodumi- PDB-6elj: FAB Fragment. AbVance: Increasing our knowledge of antibody struc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6elj | ||||||
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Title | FAB Fragment. AbVance: Increasing our knowledge of antibody structural space to enable faster and better decision making in antibody drug discovery | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY / fAB FRAGMENT / AbVance project / Pistoia Alliance | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Benz, J. / Weigand, S. / Dengl, S. / Schlothauer, T. / Auer, J. / Ehler, A. / Kettenberger, H. / Lorenz, S. / Hirschheydt, T. / Georges, G. | ||||||
Citation | Journal: To Be Published Title: AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in antibody drug discovery Authors: Benz, J. / Georges, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6elj.cif.gz | 344.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6elj.ent.gz | 281.5 KB | Display | PDB format |
PDBx/mmJSON format | 6elj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/6elj ftp://data.pdbj.org/pub/pdb/validation_reports/el/6elj | HTTPS FTP |
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-Related 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: 24570.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 23552.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #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: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Na cacodylat 6.5 pH 25 %w/v PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.24 Å / Num. obs: 67823 / % possible obs: 97.6 % / Redundancy: 3.42 % / Biso Wilson estimate: 31.03 Å2 / Rmerge(I) obs: 0.01 / Rsym value: 0.09 / Net I/σ(I): 7.55 |
Reflection shell | Resolution: 1.9→2 Å / Rsym value: 0.68 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house Fab structure Resolution: 1.9→44.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.137
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Displacement parameters | Biso mean: 35.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→44.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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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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