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- PDB-8t84: Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms hetero... -
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Open data
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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 | ||||||
![]() | Racemic mixture of amyloid beta segment 35-MVGGVV-40 | ||||||
![]() | PROTEIN FIBRIL / Rippled beta sheet / amyloid fibril | ||||||
Function / homology | 1,1,1,3,3,3-hexafluoropropan-2-ol![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sawaya, M.R. / Raskatov, J.A. / Hazari, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384 KB | Display | ![]() |
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Full document | ![]() | 384 KB | Display | |
Data in XML | ![]() | 2.1 KB | Display | |
Data in CIF | ![]() | 2.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t82C ![]() 8t86C ![]() 8t89C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein/peptide | Mass: 560.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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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