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Yorodumi- PDB-4ro8: Sequence and structure of a self-assembled 3-D DNA crystal: D(GGA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ro8 | ||||||
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Title | Sequence and structure of a self-assembled 3-D DNA crystal: D(GGAATCGATGGAG) | ||||||
Components | D(GGAATCGATGGAG) | ||||||
Keywords | DNA / Self assembling 3D DNA crystal | ||||||
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. #1: Journal: Chem.Biol. / Year: 2004 Title: Crystal structure of a continuous three-dimensional DNA lattice. Authors: Paukstelis, P.J. / Nowakowski, J. / Birktoft, J.J. / Seeman, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ro8.cif.gz | 23.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ro8.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ro8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ro8_validation.pdf.gz | 374.4 KB | Display | wwPDB validaton report |
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Full document | 4ro8_full_validation.pdf.gz | 374.4 KB | Display | |
Data in XML | 4ro8_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 4ro8_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/4ro8 ftp://data.pdbj.org/pub/pdb/validation_reports/ro/4ro8 | HTTPS FTP |
-Related structure data
Related structure data | 4rnkC 4ro4C 4ro7C 4rogC 4rokC 4ronC 4rooC 4royC 4rozC 4rp0C 4rp1C 4rp2C 1p1yS C: citing same article (ref.) S: Starting model for refinement |
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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: 4080.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA molecule synthesized on a DNA synthesizer. |
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#2: Chemical | ChemComp-MG / |
#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: 3.03 Å3/Da / Density % sol: 59.39 % |
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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→52.91 Å / Num. obs: 2873 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.08→2.19 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.7 / Num. unique all: 347 |
-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→34.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 21.241 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.986 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→34.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.077→2.131 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.018 Å / Origin y: -14.751 Å / Origin z: -12.125 Å
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