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Yorodumi- PDB-6dkl: Crystal Structure of a Rationally Designed Six-Fold Symmetric DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dkl | |||||||||
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Title | Crystal Structure of a Rationally Designed Six-Fold Symmetric DNA Scaffold | |||||||||
Components |
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Keywords | DNA / DNA Nanotechnology / Structural DNA Nanotechnology / self-assembly / crystal design / DNA crystals | |||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.034 Å | |||||||||
Authors | Simmons, C.R. / Zhang, F. / Yan, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry. Authors: Zhang, F. / Simmons, C.R. / Gates, J. / Liu, Y. / Yan, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dkl.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dkl.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 6dkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dkl_validation.pdf.gz | 386.5 KB | Display | wwPDB validaton report |
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Full document | 6dkl_full_validation.pdf.gz | 387 KB | Display | |
Data in XML | 6dkl_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 6dkl_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/6dkl ftp://data.pdbj.org/pub/pdb/validation_reports/dk/6dkl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2764.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2973.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3371.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 3687.417 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 grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50 mM Cacodylate pH 6.0, 10 mM MgCl2, 200 mM sodium citrate, 5% isopropanol Temp details: Temperature gradient was generated from 60C-25C for .3 degrees per hour. |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.034→50 Å / Num. obs: 6788 / % possible obs: 91.8 % / Redundancy: 6.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Net I/σ(I): 42.1 |
Reflection shell | Resolution: 3.034→3.1 Å / Num. unique obs: 252 / CC1/2: 0.93 / Rpim(I) all: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.034→37.1758 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 41.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.034→37.1758 Å
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Refine LS restraints |
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LS refinement shell |
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