+Open data
-Basic information
Entry | Database: PDB / ID: 8vpx | ||||||
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Title | UIC-10-BPE extension of UIC-1 | ||||||
Components | UIC-10-BPE | ||||||
Keywords | DE NOVO PROTEIN / synthetic construct | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å | ||||||
Authors | Ganatra, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Diverse Proteomimetic Frameworks via Rational Design of pi-Stacking Peptide Tectons Authors: Ganatra, P. / Wang, D.F. / Ren, Z. / Dang, V.T. / Nguyen, A.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vpx.cif.gz | 29.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vpx.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 8vpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vpx_validation.pdf.gz | 381.6 KB | Display | wwPDB validaton report |
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Full document | 8vpx_full_validation.pdf.gz | 381.6 KB | Display | |
Data in XML | 8vpx_validation.xml.gz | 3 KB | Display | |
Data in CIF | 8vpx_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/8vpx ftp://data.pdbj.org/pub/pdb/validation_reports/vp/8vpx | HTTPS FTP |
-Related structure data
Related structure data | 8vogC 8vp7C 8vpcC 8vpdC 8vpeC 8vpjC 8vpsC 8vptC 8vpyC 8vpzC 8vq0C 8vsfC 8vt8C 8vw7C 8vw8C 8vxsC 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: 1459.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.06 Å3/Da / Density % sol: 40.35 % |
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Crystal grow | Temperature: 298 K / Method: slow cooling / Details: Methanol, acetonitrile, water |
-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: 0.688839 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.688839 Å / Relative weight: 1 |
Reflection | Resolution: 1.451→17.22 Å / Num. obs: 2572 / % possible obs: 80.18 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 28.56 |
Reflection shell | Resolution: 1.451→1.502 Å / Num. unique obs: 173 / CC1/2: 0.997 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.451→17.22 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 2.14 / Phase error: 24.0318 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.98 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.451→17.22 Å
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Refine LS restraints |
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LS refinement shell |
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