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Yorodumi- PDB-6uef: Crystal Structure of a Self-Assembling DNA Scaffold Containing Se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uef | |||||||||
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Title | Crystal Structure of a Self-Assembling DNA Scaffold Containing Sequence Modifications to Attempt to Disrupt Crystal Contacts in a Rhombohedral Lattice. | |||||||||
Components |
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Keywords | DNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold | |||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uef.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uef.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 6uef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uef_validation.pdf.gz | 249.2 KB | Display | wwPDB validaton report |
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Full document | 6uef_full_validation.pdf.gz | 249.2 KB | Display | |
Data in XML | 6uef_validation.xml.gz | 946 B | Display | |
Data in CIF | 6uef_validation.cif.gz | 1.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/6uef ftp://data.pdbj.org/pub/pdb/validation_reports/ue/6uef | HTTPS FTP |
-Related structure data
Related structure data | 6u40SC 6udnC 6v6rC 6wjkC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 6407.161 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: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.44 Å3/Da / Density % sol: 72.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 mL of 0.05 M TRIS pH 8.0, 200 mM MgCl2, and 15% ethanol 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→50 Å / Num. obs: 4634 / % possible obs: 99.8 % / Redundancy: 10 % / Biso Wilson estimate: 81.21 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.03 / Rrim(I) all: 0.094 / Χ2: 2.747 / Net I/σ(I): 11.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6U40 Resolution: 2.95→23.525 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 26.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 160.12 Å2 / Biso mean: 96.081 Å2 / Biso min: 48.8 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→23.525 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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