+Open data
-Basic information
Entry | Database: PDB / ID: 8irq | ||||||
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Title | Larimichthys crocea IFNd | ||||||
Components | Interferon d | ||||||
Keywords | CYTOKINE / interferon / antiviral | ||||||
Function / homology | Function and homology information cytokine receptor binding / cytokine activity / defense response to virus / extracellular space Similarity search - Function | ||||||
Biological species | Larimichthys crocea (large yellow croaker) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Chen, J.J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of large yellow croaker IFNd at 1.49 Angstrom resolution. Authors: Chen, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8irq.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8irq.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 8irq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8irq_validation.pdf.gz | 424.4 KB | Display | wwPDB validaton report |
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Full document | 8irq_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 8irq_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 8irq_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/8irq ftp://data.pdbj.org/pub/pdb/validation_reports/ir/8irq | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18898.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Larimichthys crocea (large yellow croaker) Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4AIP8 |
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#2: 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: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 289.15 K / Method: liquid diffusion / Details: PEG 2000ME, Trisbase/Hydrochloric acid |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→47.09 Å / Num. obs: 22157 / % possible obs: 95.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 27.52 |
Reflection shell | Resolution: 1.49→1.543 Å / CC1/2: 0.999 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→47.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.979 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.083 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.859 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→47.09 Å
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Refine LS restraints |
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