+Open data
-Basic information
Entry | Database: PDB / ID: 5i6t | ||||||||||||||||||||||||||||||
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Title | Crystal structure of color device state C | ||||||||||||||||||||||||||||||
Components |
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Keywords | DNA / tensegrity triangle / single strand extending | ||||||||||||||||||||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||||||||||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.283 Å | ||||||||||||||||||||||||||||||
Authors | Hao, Y. / Birktoft, J. / Seeman, N.C. | ||||||||||||||||||||||||||||||
Funding support | United States, 9items
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Citation | Journal: Nat Chem / Year: 2017 Title: A device that operates within a self-assembled 3D DNA crystal. Authors: Hao, Y. / Kristiansen, M. / Sha, R. / Birktoft, J.J. / Hernandez, C. / Mao, C. / Seeman, N.C. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i6t.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i6t.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 5i6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/5i6t ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i6t | HTTPS FTP |
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-Related structure data
Related structure data | 5i36C 5i6qC 3gbiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 8 types, 8 molecules ABCDEFGH
#1: DNA chain | Mass: 6424.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 7853.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 4366.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 4295.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 4327.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: DNA chain | Mass: 6432.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#7: DNA chain | Mass: 6457.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#8: DNA chain | Mass: 1504.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.62 Å3/Da / Density % sol: 83.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30 mM sodium cacodylate, 50 mM magnesium acetate, 50 mM ammonium sulfate, 5 mM magnesium chloride and 25 mM Tris HCl (pH 8.5) |
-Data collection
Diffraction | Mean temperature: 80 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 5.27→50 Å / Num. obs: 4417 / % possible obs: 98.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 270.34 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.304 / Net I/av σ(I): 29.483 / Net I/σ(I): 8.5 / Num. measured all: 16778 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GBI Resolution: 5.283→41.74 Å / SU ML: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 45.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 905.58 Å2 / Biso mean: 358.3626 Å2 / Biso min: 205.99 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 5.283→41.74 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: 3
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