+Open data
-Basic information
Entry | Database: PDB / ID: 6p4y | ||||||
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Title | Crystal Structure of anti-IL-7Ralpha 4A10 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody 4A10 Fab fragment / protein polymer | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å | ||||||
Authors | Walsh, S.T.R. / Kashi, L. / Kohnhorst, C.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Leukemia / Year: 2020 Title: New anti-IL-7R alpha monoclonal antibodies show efficacy against T cell acute lymphoblastic leukemia in pre-clinical models. Authors: Hixon, J.A. / Andrews, C. / Kashi, L. / Kohnhorst, C.L. / Senkevitch, E. / Czarra, K. / Barata, J.T. / Li, W. / Schneider, J.P. / Walsh, S.T.R. / Durum, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p4y.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p4y.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 6p4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/6p4y ftp://data.pdbj.org/pub/pdb/validation_reports/p4/6p4y | HTTPS FTP |
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-Related structure data
Related structure data | 6p50C 6p67C 1ae6S S: Starting model for refinement 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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Unit cell |
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-Components
#1: Antibody | Mass: 24360.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: mouse hybridoma / Variant: C57BL/6 |
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#2: Antibody | Mass: 23606.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Variant: C57BL/6 |
#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: 2.03 Å3/Da / Density % sol: 39.33 % / Description: triangular plate |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 30% PEG 5000, 0.1 M sodium acetate, 20% glycerol, seeded Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014 / Details: K-B mirrors |
Radiation | Monochromator: K-B mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→39.248 Å / Num. obs: 36735 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1257 / Rpim(I) all: 0.08014 / Rrim(I) all: 0.1495 / Net I/σ(I): 8.33 |
Reflection shell | Resolution: 1.799→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.418 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 3613 / CC1/2: 0.42 / Rpim(I) all: 0.9215 / Rrim(I) all: 1.418 / % possible all: 96.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AE6 Resolution: 1.799→39.248 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.75 / 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: 1.799→39.248 Å
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Refine LS restraints |
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LS refinement shell |
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