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Open data
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Basic information
Entry | Database: PDB / ID: 6l9x | ||||||
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Title | Xenons in frog EPDR1 | ||||||
![]() | Ependymin-related 1 | ||||||
![]() | UNKNOWN FUNCTION / EPDR1 / Xenon | ||||||
Function / homology | Ependymin / Ependymin / Ependymins / cell-matrix adhesion / lysosome / calcium ion binding / extracellular region / XENON / Mammalian ependymin-related protein 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: De novo Phasing Xenons Observed in the Frog Ependymin-Related Protein Authors: Park, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.1 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 22836.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: epdr1 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-XE / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 6390 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.976 / Rmerge(I) obs: 0.097 / Net I/σ(I): 71 |
Reflection shell | Resolution: 2.9→2.95 Å / Rmerge(I) obs: 0.582 / Num. unique obs: 2312 / CC1/2: 0.976 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.66 Å2 / Biso mean: 63.6 Å2 / Biso min: 39.49 Å2
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Refinement step | Cycle: final / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.903→2.978 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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