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Yorodumi- PDB-8t84: Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms hetero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t84 | ||||||
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Title | Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms heterochiral rippled beta-sheet, includes hexafluoroisopropanol | ||||||
Components | Racemic mixture of amyloid beta segment 35-MVGGVV-40 | ||||||
Keywords | PROTEIN FIBRIL / Rippled beta sheet / amyloid fibril | ||||||
Function / homology | 1,1,1,3,3,3-hexafluoropropan-2-ol Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.101 Å | ||||||
Authors | Sawaya, M.R. / Raskatov, J.A. / Hazari, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets. Authors: Hazari, A. / Sawaya, M.R. / Sajimon, M. / Vlahakis, N. / Rodriguez, J. / Eisenberg, D. / Raskatov, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t84.cif.gz | 15.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t84.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8t84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/8t84 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t84 | HTTPS FTP |
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-Related structure data
Related structure data | 8t82C 8t86C 8t89C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 560.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.57 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / Details: hexafluoroisopropanol, water |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→20.981 Å / Num. obs: 2980 / % possible obs: 85.8 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.174 / Rrim(I) all: 0.186 / Net I/σ(I): 4.88 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.101→20.981 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.985 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.22 / SU B: 1.233 / SU ML: 0.027 / Average fsc free: 0.8922 / Average fsc work: 0.9273 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.041 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.652 Å2
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Refinement step | Cycle: LAST / Resolution: 1.101→20.981 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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