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Yorodumi- PDB-8gd8: Porous framework formed by assembly of a bipyridyl-conjugated hel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gd8 | |||||||||
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Title | Porous framework formed by assembly of a bipyridyl-conjugated helical peptide | |||||||||
Components | bipyridyl-conjugated helical peptide | |||||||||
Keywords | DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | |||||||||
Authors | Hess, S.S. / Nguyen, A.I. | |||||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. Authors: Hess, S.S. / Coppola, F. / Dang, V.T. / Tran, P.N. / Mickel, P.J. / Oktawiec, J. / Ren, Z. / Kral, P. / Nguyen, A.I. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gd8.cif.gz | 44 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gd8.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 8gd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gd8_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 8gd8_full_validation.pdf.gz | 423.1 KB | Display | |
Data in XML | 8gd8_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 8gd8_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/8gd8 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/8gd8 | HTTPS FTP |
-Related structure data
Related structure data | 8gb9C 8gbaC 8gbhC 8gbiC 8gbmC 8gboC 8gd6C 8givC 8gj7C 8gk1C 8gk2C 8gk9C 8gkbC 8gkxC 8gl0C 8gl4C 8gl5C 8sw2C 8sy4C C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1259.479 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.65 % |
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Crystal grow | Temperature: 298 K / Method: slow cooling / Details: Water/Acetonitrile |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.61992 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.61992 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→16.59 Å / Num. obs: 22123 / % possible obs: 88.81 % / Redundancy: 2 % / Biso Wilson estimate: 5.04 Å2 / Rmerge(I) obs: 0.04922 / Net I/σ(I): 12.47 |
Reflection shell | Resolution: 1.04→1.077 Å / Rmerge(I) obs: 0.06539 / Num. unique obs: 1210 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→16.59 Å / SU ML: 0.1049 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 28.7979 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 8.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→16.59 Å
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Refine LS restraints |
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LS refinement shell |
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