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- PDB-4e4o: Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex -
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Open data
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Basic information
Entry | Database: PDB / ID: 4e4o | ||||||
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Title | Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex | ||||||
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![]() | DNA / Z-type DNA double helices / Barium ions | ||||||
Function / homology | : / DNA![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mandal, P.K. / Venkadesh, S. / Gautham, N. | ||||||
![]() | ![]() Title: Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.9 KB | Display | ![]() |
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PDB format | ![]() | 15.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.7 KB | Display | ![]() |
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Full document | ![]() | 391.1 KB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 4.9 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: 1794.206 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 1825.216 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-BA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.5809 Å3/Da / Density % sol: 22.1971 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: drop: 1mM of duplex DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM barium dichloride dihydrate, 0.5mM spermine, reservoir: 30% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, ...Details: drop: 1mM of duplex DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM barium dichloride dihydrate, 0.5mM spermine, reservoir: 30% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 6, 2010 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→25 Å / Num. all: 4897 / Num. obs: 4873 / % possible obs: 99.5 % / Redundancy: 4.71 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.0384 / Rsym value: 0.0357 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 4.68 % / Rmerge(I) obs: 0.2076 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.1908 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: fiber model of Z-type DNA built using the program InsightII Resolution: 1.72→23.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.645 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→23.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.764 Å / Total num. of bins used: 20
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