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Open data
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Basic information
Entry | Database: PDB / ID: 7y5r | ||||||
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Title | Crystal structure of sDscam FNIII2 domain, isoform alpha7 | ||||||
![]() | Down Syndrome Cell Adhesion Molecules | ||||||
![]() | CELL ADHESION / cell surface receptor | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Q. / Yu, Y. / Cheng, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the self-recognition of sDSCAM in Chelicerata. Authors: Cheng, J. / Yu, Y. / Wang, X. / Zheng, X. / Liu, T. / Hu, D. / Jin, Y. / Lai, Y. / Fu, T.M. / Chen, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 39.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y4xC ![]() 7y54C ![]() 7y5jC ![]() 7y6eC ![]() 7y6oC ![]() 7y73C ![]() 7y8hC ![]() 7y8iC ![]() 7y8sC ![]() 7y95C ![]() 7y9aC ![]() 1va9S S: Starting model for refinement C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 11477.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.6 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES sodium pH 7.5, 1.5 M Lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2020 | ||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→50 Å / Num. obs: 13917 / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.051 / Rrim(I) all: 0.181 / Χ2: 0.985 / Net I/σ(I): 13.9 | ||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VA9 Resolution: 1.562→26.64 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.6 / 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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 71.44 Å2 / Biso mean: 15.9402 Å2 / Biso min: 5.2 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.562→26.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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