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Yorodumi- PDB-4rnk: Sequence and structure of a self-assembled 3-D DNA crystal: D(GGA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rnk | ||||||
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Title | Sequence and structure of a self-assembled 3-D DNA crystal: D(GGAAAATTTGGAG) | ||||||
Components | GGAAAATTTGGAG | ||||||
Keywords | DNA / 3D DNA Lattice | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Saoji, M.M. / Paukstelis, P.J. | ||||||
Citation | Journal: Biopolymers / Year: 2015 Title: Probing the role of sequence in the assembly of three-dimensional DNA crystals. Authors: Saoji, M. / Zhang, D. / Paukstelis, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rnk.cif.gz | 23.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rnk.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rnk_validation.pdf.gz | 366.2 KB | Display | wwPDB validaton report |
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Full document | 4rnk_full_validation.pdf.gz | 366.1 KB | Display | |
Data in XML | 4rnk_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 4rnk_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/4rnk ftp://data.pdbj.org/pub/pdb/validation_reports/rn/4rnk | HTTPS FTP |
-Related structure data
Related structure data | 4ro4C 4ro7C 4ro8C 4rogC 4rokC 4ronC 4rooC 4royC 4rozC 4rp0C 4rp1C 4rp2C 1p1yS 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 on special symmetry positions |
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Details | This DNA monomer self assembles in presence of divalent cations to form 3D DNA crystals. |
-Components
#1: DNA chain | Mass: 4079.684 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The DNA sample was synthesized using a DNA synthesizer. | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.66 % |
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Crystal grow | Temperature: 298 K / Method: evaporation Details: 120mM Magnesium Formate 50mM Lithium Chloride 10% MPD, pH none, EVAPORATION, temperature 298K PH range: none |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→55.99 Å / Num. obs: 3045 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 2.08→2.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / Num. unique all: 426 |
-Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P1Y Resolution: 2.08→34.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 11.485 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.531 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→34.41 Å
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Refine LS restraints |
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