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- PDB-6dez: Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dez | ||||||
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Title | Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate | ||||||
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Function / homology | ![]() ![]() ![]() ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Antibody | ||||||
![]() | Mou, K. / Leung, K. / Wells, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering Improved Antiphosphotyrosine Antibodies Based on an Immunoconvergent Binding Motif. Authors: Mou, Y. / Zhou, X.X. / Leung, K. / Martinko, A.J. / Yu, J.Y. / Chen, W. / Wells, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.8 KB | Display | ![]() |
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PDB format | ![]() | 130.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6df0C ![]() 6df1C ![]() 6df2C ![]() 1bj1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 26951.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() ![]() #2: Antibody | Mass: 28786.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.02 % / Mosaicity: 1.1 ° |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG4000 and 0.336M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2016 |
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromator (DCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→74.3 Å / Num. obs: 20773 / % possible obs: 99.9 % / Redundancy: 17.9 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.143 / Rrim(I) all: 0.373 / Net I/σ(I): 4.8 / Num. measured all: 397240 / Scaling rejects: 202 |
Reflection shell | Resolution: 3.2→3.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.454 / Num. unique obs: 4345 / CC1/2: 0.105 / Rpim(I) all: 2.758 / Rrim(I) all: 6.731 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1bj1 Resolution: 3.2→19.999 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.99 / 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: 3.2→19.999 Å
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Refine LS restraints |
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LS refinement shell |
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