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Open data
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Basic information
Entry | Database: PDB / ID: 5w1z | ||||||||||||||||||||
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Title | Crystal Structure of inosine-substituted decamer duplex DNA (I4) | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Inosine / DNA crystal structure / deoxyinonsine / circular dichroism of modified DNA | Function / homology | DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Pallan, P.S. / Egli, M. | ![]() ![]() Title: Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography. Authors: Peters, J.P. / Kowal, E.A. / Pallan, P.S. / Egli, M. / Maher 3rd., L.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 | ![]() | 57.5 KB | Display | ![]() |
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PDB format | ![]() | 42.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.4 KB | Display | ![]() |
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Full document | ![]() | 406 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3050.807 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.87 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Droplets (2 uL) containing oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), magnesium acetate (12.5 mM), and MPD (20% v/v) that were equilibrated against a 1 mL reservoir of ...Details: Droplets (2 uL) containing oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), magnesium acetate (12.5 mM), and MPD (20% v/v) that were equilibrated against a 1 mL reservoir of sodium cacodylate (50 mM, pH 6.5), magnesium acetate (25 mM), and MPD (40% v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→32.24 Å / Num. obs: 13618 / % possible obs: 97.1 % / Observed criterion σ(I): 5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.053 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1 / Num. unique obs: 640 / Rpim(I) all: 0.434 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.471 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→32.24 Å
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Refine LS restraints |
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