+Open data
-Basic information
Entry | Database: PDB / ID: 3s34 | ||||||
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Title | Structure of the 1121B Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / VEGF receptor domain 3 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Franklin, M.C. | ||||||
Citation | Journal: Structure / Year: 2011 Title: The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies. Authors: Franklin, M.C. / Navarro, E.C. / Wang, Y. / Patel, S. / Singh, P. / Zhang, Y. / Persaud, K. / Bari, A. / Griffith, H. / Shen, L. / Balderes, P. / Kussie, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s34.cif.gz | 180.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s34.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/3s34 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/3s34 | HTTPS FTP |
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-Related structure data
Related structure data | 3s35C 3s36C 3s37C 1yy9S C: citing same article (ref.) S: Starting model for refinement |
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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: 23245.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23324.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.79 Å3/Da / Density % sol: 55.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Na/K phosphate, pH 5.5, 40% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 22, 2008 |
Radiation | Monochromator: Rigaku VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→70 Å / Num. all: 27477 / Num. obs: 26790 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.06 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.5 / % possible all: 78.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YY9 Resolution: 2.2→50.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.662 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.381 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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