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- PDB-5bz7: X-ray crystal structure of a continuously hydrogen bonded 14mer D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bz7 | ||||||||||||||||||||
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Title | X-ray crystal structure of a continuously hydrogen bonded 14mer DNA lattice. | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / 3D DNA lattice / 14mer DNA / Self assembly | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Saoji, M. / Paukstelis, P.J. | ![]() ![]() Title: Sequence-dependent structural changes in a self-assembling DNA oligonucleotide. Authors: Saoji, M. / Paukstelis, P.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 18.8 KB | Display | ![]() |
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PDB format | ![]() | 11 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 346.4 KB | Display | ![]() |
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Full document | ![]() | 346.4 KB | Display | |
Data in XML | ![]() | 2.3 KB | Display | |
Data in CIF | ![]() | 2.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bxwSC ![]() 5bz9C ![]() 5bzyC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Components
#1: DNA chain | Mass: 4392.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, sitting drop Details: 120mM Magnesium Formate 50mM Lithium Chloride 10% MPD |
-Data collection
Diffraction | Mean temperature: 77.15 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / 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: 2.03→22.53 Å / Num. obs: 3436 / % possible obs: 99.4 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.03→2.09 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BXW Resolution: 2.03→22.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.263 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.196 / 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: 57.957 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→22.53 Å
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Refine LS restraints |
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