+Open data
-Basic information
Entry | Database: PDB / ID: 4x7t | ||||||||||||
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Title | Structure of Omalizumab Fab fragment, crystal form 2 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody Fab Fragment / Anti-IgE antibody / Anti-inflammatory | ||||||||||||
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: 3 Å | ||||||||||||
Authors | Jensen, R.K. / Andersen, G.R. | ||||||||||||
Funding support | Denmark, 3items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Structure of the omalizumab Fab Authors: Jensen, R.K. / Plum, M. / Tjerrild, L. / Jakob, T. / Spillner, E. / Andersen, G.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x7t.cif.gz | 344.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x7t.ent.gz | 282.9 KB | Display | PDB format |
PDBx/mmJSON format | 4x7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7t ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7t | HTTPS FTP |
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-Related structure data
Related structure data | 4x7sSC 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23653.387 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: 23922.287 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: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, Polyvinyl Pyrrolidone K15, Lithium Sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97551 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97551 Å / Relative weight: 1 |
Reflection | Resolution: 3→45.41 Å / Num. obs: 19417 / % possible obs: 99.37 % / Redundancy: 3.4 % / Rsym value: 0.202 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3→3.107 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.11 / % possible all: 99.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X7S Resolution: 3→45.408 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.32 / 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: 3→45.408 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.6159 Å / Origin y: -3.0265 Å / Origin z: 18.1444 Å
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Refinement TLS group | Selection details: all |