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- PDB-363d: High-resolution crystal structure of a fully modified N3'-> P5' p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 363d | ||||||||||||||||||
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Title | High-resolution crystal structure of a fully modified N3'-> P5' phosphoramidate DNA dodecamer duplex | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / A-DNA / MODIFIED | Function / homology | AMMONIUM ION / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Tereshko, V. / Gryaznov, S. / Egli, M. | ![]() Journal: J.Am.Chem.Soc. / Year: 1998 | Title: Consequences of Replacing the DNA 3'-Oxygen by an Amino Group: High-Resolution Crystal Structure of a Fully Modified N3'--> P5' Phosphoramidate DNA Dodecamer Duplex Authors: Tereshko, V. / Gryaznov, S. / 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 | ![]() | 57.8 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar 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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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3652.559 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source #2: Chemical | ChemComp-NH4 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, sitting drop / PH range low: 7.4 / PH range high: 6.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→34 Å / Num. obs: 6737 / % possible obs: 98.4 % / Rmerge(I) obs: 0.082 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 11.4 % |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 34 Å / % possible obs: 98.4 % / Num. measured all: 76542 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: A-FORM DUPLEX Resolution: 2→8 Å / Cross valid method: FREE R-VALUE / σ(F): 2 Details: THE CRYSTAL IS A PRECISE MEROHEDRAL TWIN AND THE COORDINATES REPRESENT ONE COLUMN CONSISTING OF THREE DODECAMER DUPLEXES (ALL ATOMS WITH OCCUPANCY 0.5, HALF THE WATERS HAVE OCCUPANCY 1.0, ...Details: THE CRYSTAL IS A PRECISE MEROHEDRAL TWIN AND THE COORDINATES REPRESENT ONE COLUMN CONSISTING OF THREE DODECAMER DUPLEXES (ALL ATOMS WITH OCCUPANCY 0.5, HALF THE WATERS HAVE OCCUPANCY 1.0, THE OTHER HALF ZERO). TOTAL NUMBER OF SOLVENT ATOMS REFERS TO R3 ASYMMETRIC UNIT.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 15 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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