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Open data
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Basic information
Entry | Database: PDB / ID: 5w20 | ||||||||||||||||||||
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Title | Crystal Structure of inosine-substituted duplex DNA | ||||||||||||||||||||
![]() | 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 | ![]() | 28.5 KB | Display | ![]() |
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PDB format | ![]() | 18.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.3 KB | Display | ![]() |
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Full document | ![]() | 387.4 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 7.6 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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Unit cell |
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Components
#1: DNA chain | Mass: 3015.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Droplets (2 uL) containing oligonucleotide (0.23 mM), sodium cacodylate (25 mM, pH 6.5), magnesium acetate (12.5 mM), and 2-methyl-2,4-pentanediol (MPD, 20% v/v) that were equilibrated ...Details: Droplets (2 uL) containing oligonucleotide (0.23 mM), sodium cacodylate (25 mM, pH 6.5), magnesium acetate (12.5 mM), and 2-methyl-2,4-pentanediol (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) PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2015 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 11019 / % possible obs: 99.1 % / Observed criterion σ(I): 5 / Redundancy: 7.7 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Net I/σ(I): 30.57 |
Reflection shell | Resolution: 1.36→1.41 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.343 / Num. unique obs: 1002 / Rpim(I) all: 0.133 / % possible all: 95 |
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Processing
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Refinement | Resolution: 1.36→26.73 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.87 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.216 Å2
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Refinement step | Cycle: 1 / Resolution: 1.36→26.73 Å
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