+Open data
-Basic information
Entry | Database: PDB / ID: 5vy7 | ||||||
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Title | A self-assembling L-form DNA crystal lattice | ||||||
Components |
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Keywords | DNA / DNA nanotechnology / self-assembly / DNA structure | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Simmons, C.R. / Yan, H. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. Authors: Simmons, C.R. / Zhang, F. / MacCulloch, T. / Fahmi, N. / Stephanopoulos, N. / Liu, Y. / 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 | 5vy7.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vy7.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 5vy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vy7 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vy7 | 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: 6466.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 1769.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2129.409 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: 5.91 Å3/Da / Density % sol: 79.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50 mM cacodylate pH 6.5, 50 mM MgCl2, 2.0 mM cobalt(III)hexamine, and 1.5 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→34.292 Å / Num. obs: 4949 / % possible obs: 86.1 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.6 / % possible all: 53.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→34.29 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 37.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→34.29 Å
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Refine LS restraints |
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LS refinement shell |
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