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- PDB-8f40: Engineering Crystals with Tunable Symmetries from 14- or 16-Base-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8f40 | |||||||||||||||
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Title | Engineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands | |||||||||||||||
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![]() | DNA / Four-Fold Rotational Axis / Left-Handed / Parallel | |||||||||||||||
Function / homology | DNA![]() | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Zhang, C. / Zhao, J. / Lu, B. / Sha, R. / Seeman, N.C. / Noinaj, N. / Mao, C. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions. Authors: Zhang, C. / Zhao, J. / Lu, B. / Seeman, N.C. / Sha, R. / Noinaj, N. / Mao, C. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.8 KB | Display | ![]() |
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PDB format | ![]() | 18 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.5 KB | Display | ![]() |
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Full document | ![]() | 377.4 KB | Display | |
Data in XML | ![]() | 2.4 KB | Display | |
Data in CIF | ![]() | 2.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ep8C ![]() 8epbC ![]() 8epdC ![]() 8epeC ![]() 8epfC ![]() 8epgC ![]() 8epiC ![]() 8f42C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: DNA chain | Mass: 1470.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 1866.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1470.998 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: 3.64 Å3/Da / Density % sol: 66.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 30 uM 0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium pH 7.0, 0.16 M lithium sulfate monohydrate, 6 % MPD at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→36.78 Å / Num. obs: 2497 / % possible obs: 87.2 % / Redundancy: 10.5 % / CC1/2: 1 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.45→2.94 Å / Redundancy: 10.7 % / Num. unique obs: 201 / CC1/2: 0.951 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ideal B type DNA duplexes generated in Cadnano Resolution: 2.45→36.78 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3921 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.57 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→36.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→36.78 Å
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Refinement TLS params. | Method: refined / Origin x: -7.99674198972 Å / Origin y: 10.9892515811 Å / Origin z: -6.59293319297 Å
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Refinement TLS group | Selection details: all |