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Open data
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Basic information
Entry | Database: PDB / ID: 6udr | |||||||||
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Title | S2 symmetric peptide design number 3 crystal form 1, Lurch | |||||||||
![]() | S2-3, Lurch crystal form 1 | |||||||||
![]() | DE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L and D-amino acids | |||||||||
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 | ![]() | 11.9 KB | Display | ![]() |
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PDB format | ![]() | 6.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385.9 KB | Display | ![]() |
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Full document | ![]() | 385.8 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 1.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ucxC ![]() 6ud9C ![]() 6udwC ![]() 6udzC ![]() 6uf4C ![]() 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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Unit cell |
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Components
#1: Protein/peptide | Mass: 1215.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
Compound details | Crystallographic symmetry operator -x,-y,-z generates the C-terminal half of the cyclic peptide ...Crystallographic symmetry operator -x,-y,-z generates the C-terminal half of the cyclic peptide Q(DTH)(DAR)(DPR)(DAS) |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M trisodium citrate, pH 6.5 |
-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: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1→11.52 Å / Num. obs: 2461 / % possible obs: 75 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.08 / Rrim(I) all: 0.151 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.05→1.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.145 / Num. measured all: 1742 / Num. unique obs: 515 / CC1/2: 0.961 / Rpim(I) all: 0.095 / Rrim(I) all: 0.175 / Net I/σ(I) obs: 8 / % possible all: 62 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1→11.52 Å / SU ML: 0.0451 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 7.6413
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 1.44 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→11.52 Å /
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Refine LS restraints |
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LS refinement shell |
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