+Open data
-Basic information
Entry | Database: PDB / ID: 6yhq | ||||||
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Title | Crystal Structure of Fab F5.18.6, anti-Plasmodium vivax AMA1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin / Fab / Malaria / AMA1 / Plasmodium | ||||||
Function / homology | THIOCYANATE ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Bentley, G.A. / Saul, F.A. / Vulliez-le Normand, B. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of Fab F5.18.6, anti-Plasmodium vivax AMA1 Authors: Bentley, G.A. / Saul, F.A. / Vulliez-le Normand, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yhq.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yhq.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yhq_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 6yhq_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 6yhq_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 6yhq_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/6yhq ftp://data.pdbj.org/pub/pdb/validation_reports/yh/6yhq | HTTPS FTP |
-Related 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: 23616.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 22860.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SCN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.18M KSCN, 16% PEG4000, 0.005M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→73.32 Å / Num. obs: 36659 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.053 / Rrim(I) all: 0.142 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.89→1.99 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5255 / CC1/2: 0.415 / Rpim(I) all: 0.381 / Rrim(I) all: 0.942 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CLO, 1QKZ Resolution: 1.89→36 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.142
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Displacement parameters | Biso max: 84.13 Å2 / Biso mean: 29.03 Å2 / Biso min: 11.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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