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- PDB-4rog: Sequence and structure of a self-assembled 3-D DNA crystal: D(GGA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rog | ||||||
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Title | Sequence and structure of a self-assembled 3-D DNA crystal: D(GGACACGTGGGAG) | ||||||
![]() | D(GGACACGTGGGAG) | ||||||
![]() | DNA / Self-assembling 3D DNA crystal | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saoji, M.M. / Paukstelis, P.J. | ||||||
![]() | ![]() Title: Probing the role of sequence in the assembly of three-dimensional DNA crystals. Authors: Saoji, M. / Zhang, D. / Paukstelis, P.J. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23 KB | Display | ![]() |
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PDB format | ![]() | 16 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.9 KB | Display | ![]() |
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Full document | ![]() | 367.9 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 2.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rnkC ![]() 4ro4C ![]() 4ro7C ![]() 4ro8C ![]() 4rokC ![]() 4ronC ![]() 4rooC ![]() 4royC ![]() 4rozC ![]() 4rp0C ![]() 4rp1C ![]() 4rp2C ![]() 1p1yS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 4081.660 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.88 % |
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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: ![]() ![]() ![]() |
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→29 Å / Num. obs: 2578 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.08→2.2 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.4 / Num. unique all: 321 |
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Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1p1y Resolution: 2.08→20.744 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / SU B: 17.477 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.666 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→20.744 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.084→2.137 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.118 Å / Origin y: -14.656 Å / Origin z: -12.099 Å
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