+Open data
-Basic information
Entry | Database: PDB / ID: 6arp | |||||||||
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Title | Structure of a mutant Cetuximab Fab fragment | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Erbitux / antibody / EGFR | |||||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / immune response / extracellular space / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Christie, M. / Christ, D. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: To Be Published Title: Structure of a mutant Cetuximab Fab fragment Authors: Christie, M. / Christ, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6arp.cif.gz | 352.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6arp.ent.gz | 286 KB | Display | PDB format |
PDBx/mmJSON format | 6arp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6arp_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 6arp_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 6arp_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 6arp_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/6arp ftp://data.pdbj.org/pub/pdb/validation_reports/ar/6arp | HTTPS FTP |
-Related structure data
Related structure data | 1yy8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Antibody | Mass: 23504.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0 #2: Antibody | Mass: 23829.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: 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: 2.99 Å3/Da / Density % sol: 58.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium citrate, 1.6 M ammonium sulfate, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.42 Å / Num. obs: 124960 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 16.2 |
Reflection shell | Redundancy: 6.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5833 / CC1/2: 0.675 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YY8 Resolution: 1.7→47.42 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.974 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 25.786 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→47.42 Å
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Refine LS restraints |
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