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Open data
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Basic information
Entry | Database: PDB / ID: 6uf4 | |||||||||
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Title | S2 symmetric peptide design number 4 crystal form 2, Pugsley | |||||||||
![]() | S2-4, Pusgley crystal form 2 | |||||||||
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Function / homology | polypeptide(D)![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
Model details | S2 symmetric cyclic peptide | |||||||||
![]() | Mulligan, V.K. / Kang, C.S. / Antselovich, I. / Sawaya, M.R. / Yeates, T.O. / Baker, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Computational design of mixed chirality peptide macrocycles with internal symmetry. Authors: Mulligan, V.K. / Kang, C.S. / Sawaya, M.R. / Rettie, S. / Li, X. / Antselovich, I. / Craven, T.W. / Watkins, A.M. / Labonte, J.W. / DiMaio, F. / Yeates, T.O. / Baker, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 16 KB | Display | ![]() |
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PDB format | ![]() | 11.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ucxC ![]() 6ud9C ![]() 6udrC ![]() 6udwC ![]() 6udzC ![]() 6uf7C ![]() 6uf8C ![]() 6uf9C ![]() 6ufaC ![]() 6ufuC ![]() 6ug2C ![]() 6ug3C ![]() 6ug6C ![]() 6ugbC ![]() 6ugcC C: citing same article ( |
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Similar structure data |
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Links
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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: Polypeptide(D) | Mass: 1120.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ab initio design / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | ![]() Compound details | The asymmetric unit contains half of the molecule. The second half is generated by a ...The asymmetric unit contains half of the molecule. The second half is generated by a crystallographic symmetry operator. | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.58 Å3/Da / Density % sol: 22.25 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate |
-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: Mar 22, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→16.033 Å / Num. obs: 5355 / % possible obs: 94.3 % / Redundancy: 5.815 % / Biso Wilson estimate: 0.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.065 / Χ2: 0.992 / Net I/σ(I): 19.14 / Num. measured all: 31141 / Scaling rejects: 200 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 6.5 Å2 / Biso mean: 1.178 Å2 / Biso min: 0.05 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.1→16.033 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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