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Yorodumi- PDB-8f42: Engineering Crystals with Tunable Symmetries from 14- or 16-Base-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f42 | |||||||||||||||||||||||||||||||||||||
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Title | Engineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands | |||||||||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Four-Fold Rotational Axis / Left-Handed / Parallel | Function / homology | Chem-HT1 / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | Authors | Zhang, C. / Zhao, J. / Lu, B. / Sha, R. / Seeman, N.C. / Noinaj, N. / Mao, C. | Funding support | United States, 4items |
Citation | Journal: J.Am.Chem.Soc. / Year: 2023 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f42.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f42.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 8f42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f42_validation.pdf.gz | 584.5 KB | Display | wwPDB validaton report |
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Full document | 8f42_full_validation.pdf.gz | 585.8 KB | Display | |
Data in XML | 8f42_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 8f42_validation.cif.gz | 4.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/8f42 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/8f42 | HTTPS FTP |
-Related structure data
Related structure data | 8ep8C 8epbC 8epdC 8epeC 8epfC 8epgC 8epiC 8f40C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4898.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-HT1 / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 30 uM motif 60 uM Hoechst 33342, 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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
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: 2.55→35.363 Å / Num. obs: 4231 / % possible obs: 80 % / Redundancy: 6.5 % / CC1/2: 1 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.55→2.93 Å / Num. unique obs: 396 / CC1/2: 0.743 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ideal B type DNA duplexes generated in Cadnano Resolution: 2.55→35.36 Å / SU ML: 0.3376 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1347 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: 54.37 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→35.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→35.36 Å
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Refinement TLS params. | Method: refined / Origin x: 8.55046629729 Å / Origin y: -8.64607123775 Å / Origin z: -12.8374923827 Å
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Refinement TLS group | Selection details: all |