+Open data
-Basic information
Entry | Database: PDB / ID: 3dif | ||||||
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Title | Crystal structure of FabOX117 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody fragments / Fabs / Transient expression / Structural Genomics / Oxford Protein Production Facility / OPPF / Immunoglobulin domain | ||||||
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: 2.4 Å | ||||||
Authors | Nettleship, J.E. / Ren, J. / Owens, R.J. / Oxford Protein Production Facility (OPPF) | ||||||
Citation | Journal: Protein Expr.Purif. / Year: 2008 Title: A pipeline for the production of antibody fragments for structural studies using transient expression in HEK 293T cells. Authors: Nettleship, J.E. / Ren, J. / Rahman, N. / Berrow, N.S. / Hatherley, D. / Barclay, A.N. / Owens, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dif.cif.gz | 180.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dif.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dif_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 3dif_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | 3dif_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3dif_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/3dif ftp://data.pdbj.org/pub/pdb/validation_reports/di/3dif | HTTPS FTP |
-Related structure data
Related structure data | 3dggSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 3
NCS ensembles :
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-Components
#1: Antibody | Mass: 23660.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pOPINVL / Cell line (production host): HEK293T / Organ (production host): Human embryonic kidney cells / Production host: Homo sapiens (human) #2: Antibody | Mass: 24772.779 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pOPINVH / Cell line (production host): HEK293T / Organ (production host): Human embryonic kidney cells / Production host: Homo sapiens (human) #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF ENTITIES 1 AND 2 WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCE OF ENTITIES 1 AND 2 WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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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: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 85% of 0.2M Ammonium sulfate, 30% w/v PEG 4000 in 15% water - with 10 microliters of 1M NaOH per 1ml crystallization solution, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 35860 / % possible obs: 97.7 % / Observed criterion σ(I): -1.5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3531 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DGG Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.874 / SU B: 15.374 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.565 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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