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- PDB-6wjk: Crystal Structure of a Self-Assembling DNA Crystal Scaffold with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wjk | |||||||||
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Title | Crystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry | |||||||||
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![]() | DNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold | |||||||||
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: A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail. Authors: Simmons, C.R. / MacCulloch, T. / Zhang, F. / Liu, Y. / 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 | ![]() | 61.3 KB | Display | ![]() |
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PDB format | ![]() | 45.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6u40SC ![]() 6udnC ![]() 6uefC ![]() 6v6rC 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: 9718.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2146.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 6207.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.6 Å3/Da / Density % sol: 83.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50 mM sodium cacodylate pH 7.0 with 20 mM MgCl2, 1.0 mM spermine, 1.0 mM CoH18N6, and 15% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.5→50 Å / Num. obs: 3195 / % possible obs: 95.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.034 / Rrim(I) all: 0.104 / Χ2: 4.623 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6U40 Resolution: 4.514→45.978 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 35.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 589.29 Å2 / Biso min: 112.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.514→45.978 Å
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Refine LS restraints |
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