+Open data
-Basic information
Entry | Database: PDB / ID: 5keo | ||||||
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Title | Structure Determination of a Self-Assembling DNA Crystal | ||||||
Components |
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Keywords | DNA / Structural DNA Nanoechnology / self-assembled crystals / self-assembly | ||||||
Function / homology | CACODYLATE ION / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Endothia gyrosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å | ||||||
Authors | Simmons, C.R. / Birktoft, J.J. / Seeman, N.C. / Yan, H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Construction and Structure Determination of a Three-Dimensional DNA Crystal. Authors: Simmons, C.R. / Zhang, F. / Birktoft, J.J. / Qi, X. / Han, D. / Liu, Y. / Sha, R. / Abdallah, H.O. / Hernandez, C. / Ohayon, Y.P. / Seeman, N.C. / Yan, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5keo.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5keo.ent.gz | 21.5 KB | Display | PDB format |
PDBx/mmJSON format | 5keo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/5keo ftp://data.pdbj.org/pub/pdb/validation_reports/ke/5keo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6426.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) |
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#2: DNA chain | Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) |
#3: DNA chain | Mass: 2761.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) |
#4: DNA chain | Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) |
#5: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM cacodylate pH 6.5, 100 mM MgCl2, 1.0 mM Cobalt(III)hexamine, and 2.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.986 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.986 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→41.61 Å / Num. obs: 2899 / % possible obs: 99.7 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 71.2 |
Reflection shell | Highest resolution: 3.15 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 19.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 3.15→41.61 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.64 / 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 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→41.61 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 3.15 Å
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