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Open data
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Basic information
Entry | Database: PDB / ID: 6wra | ||||||||||||
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Title | Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J34 immobile Holliday junction | ||||||||||||
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![]() | DNA / Structural DNA nanotechnology / immobile Holliday junctions / 3D DNA self-assembly / designer DNA crystals | ||||||||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. Authors: Simmons, C.R. / MacCulloch, T. / Krepl, M. / Matthies, M. / Buchberger, A. / Crawford, I. / Sponer, J. / Sulc, P. / Stephanopoulos, N. / Yan, H. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.9 KB | Display | ![]() |
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PDB format | ![]() | 22.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.8 KB | Display | ![]() |
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Full document | ![]() | 392.1 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wqgC ![]() 6wr3C ![]() 6wr5C ![]() 6wr7C ![]() 6wr9C ![]() 6wrbC ![]() 6wrcC ![]() 6wriC ![]() 6wrjC ![]() 6wsnC ![]() 6wsoC ![]() 6wspC ![]() 6wsqC ![]() 6wsrC ![]() 6wssC ![]() 6wstC ![]() 6wsuC ![]() 6wsvC ![]() 6wswC ![]() 6wsxC ![]() 6wsyC ![]() 6wszC ![]() 6wt0C ![]() 6wt1C ![]() 6x8bC ![]() 6x8cC ![]() 6xdvC ![]() 6xdwC ![]() 6xdxC ![]() 6xdyC ![]() 6xdzC ![]() 6xeiC ![]() 6xejC ![]() 6xekC ![]() 6xelC ![]() 6xemC ![]() 6xfcC ![]() 6xfdC ![]() 6xfeC ![]() 6xffC ![]() 6xfgC ![]() 6xfwC ![]() 6xfxC ![]() 6xfyC ![]() 6xfzC ![]() 6xg0C ![]() 6xgjC ![]() 6xgkC ![]() 6xglC ![]() 6xgmC ![]() 6xgnC ![]() 6xgoC ![]() 6xnaC ![]() 6xo5C ![]() 6xo6C ![]() 6xo7C ![]() 6xo8C ![]() 6xo9C ![]() 7jftC ![]() 7jfuC ![]() 7jfvC ![]() 7jfwC ![]() 7jfxC ![]() 7jh8C ![]() 7jh9C ![]() 7jhaC ![]() 7jhbC ![]() 7jhcC ![]() 7jhrC ![]() 7jhsC ![]() 7jhtC ![]() 7jhuC ![]() 7jhvC ![]() 7ji5C ![]() 7ji6C ![]() 7ji7C ![]() 7ji8C ![]() 7ji9C ![]() 7jimC ![]() 7jinC ![]() 7jioC ![]() 7jipC ![]() 7jiqC ![]() 7jj2C ![]() 7jj3C ![]() 7jj4C ![]() 7jj5C ![]() 7jj6C ![]() 7jjwC ![]() 7jjxC ![]() 7jjyC ![]() 7jjzC ![]() 7jk0C ![]() 7jkdC ![]() 7jkeC ![]() 7jkgC ![]() 7jkhC ![]() 7jkiC ![]() 7jkjC ![]() 7jkkC ![]() 7jl9C ![]() 7jlaC ![]() 7jlbC ![]() 7jlcC ![]() 7jldC ![]() 7jleC ![]() 7jlfC ![]() 7jnjC ![]() 7jnkC ![]() 7jnlC ![]() 7jnmC ![]() 7jogC ![]() 7johC ![]() 7joiC ![]() 7jojC ![]() 7jokC ![]() 7jolC ![]() 7jonC ![]() 7jp5C ![]() 7jp6C ![]() 7jp7C ![]() 7jp8C ![]() 7jp9C ![]() 7jpaC ![]() 7jpbC ![]() 7jpcC ![]() 7jryC ![]() 7jrzC ![]() 7js0C ![]() 7js1C ![]() 7js2C ![]() 7jsbC ![]() 7jscC ![]() 5kekS S: Starting model for refinement 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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Unit cell |
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Components
#1: DNA chain | Mass: 6410.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA chain | Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 2786.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#4: DNA chain | Mass: 2104.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#5: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.38 Å3/Da / Density % sol: 80.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 mL of 0.05 M HEPES pH 7.5 with 20 mM MgCl2, 1.0 mM spermine, and 5% PEG 8000 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 6287 / % possible obs: 99.4 % / Redundancy: 5.8 % / CC1/2: 0.911 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.059 / Rrim(I) all: 0.144 / Χ2: 1.742 / Net I/σ(I): 8.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KEK Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.964 / SU B: 13.784 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.28 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 239.08 Å2 / Biso mean: 96.477 Å2 / Biso min: 41.26 Å2
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Refinement step | Cycle: final / Resolution: 3→50 Å
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LS refinement shell | Resolution: 3.001→3.079 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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