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- PDB-1ei4: B-DNA DODECAMER CGCGAAT(TLC)CGCG WITH INCORPORATED [3.3.0]BICYCLO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ei4 | ||||||||||||||||||
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Title | B-DNA DODECAMER CGCGAAT(TLC)CGCG WITH INCORPORATED [3.3.0]BICYCLO-ARABINO-THYMINE-5'-PHOSPHATE | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / MODIFIED B-DODECAMER / [3.3.0]BICYCLO-ARABINONUCLEIC ACID | Function / homology | SPERMINE / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Minasov, G. / Teplova, M. / Nielsen, P. / Wengel, J. / Egli, M. | ![]() ![]() Title: Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA. Authors: Minasov, G. / Teplova, M. / Nielsen, P. / Wengel, J. / Egli, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.7 KB | Display | ![]() |
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PDB format | ![]() | 18.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 401.7 KB | Display | ![]() |
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Full document | ![]() | 402.8 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 3747.466 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.41 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: OLIGONUCLEOTIDE, SPERMINE, MAGNESIUM ACETATE, SODIUM CACODYLATE BUFFER, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→20 Å / Num. all: 13592 / Num. obs: 13592 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 44.4 |
Reflection shell | Resolution: 1.43→1.48 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.188 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 115296 |
Reflection shell | *PLUS % possible obs: 99.2 % |
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Processing
Software |
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Refinement | Resolution: 1.43→17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL. Details: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES, BULK SOLVENT CORRECTION
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.43→17 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 17 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |