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Open data
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Basic information
Entry | Database: PDB / ID: 1dnt | ||||||||||||||||||
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Title | RNA/DNA DODECAMER R(GC)D(GTATACGC) WITH MAGNESIUM BINDING SITES | ||||||||||||||||||
![]() | DNA/RNA (5'-R(*![]() DNA-RNA HYBRID / DNA CONFORMATION / RNA/DNA HYBRID / METAL IONS / DNA-RNA COMPLEX / DNA-RNA HYBRID COMPLEX | Function / homology | DNA/RNA hybrid | ![]() Method | ![]() ![]() ![]() Robinson, H. / Gao, Y.-G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J. | ![]() ![]() Title: Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes. Authors: Robinson, H. / Gao, Y.G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.7 KB | Display | ![]() |
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PDB format | ![]() | 13.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.7 KB | Display | ![]() |
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Full document | ![]() | 368.4 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 4.3 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/RNA hybrid | Mass: 3077.005 Da / Num. of mol.: 2 / Source method: obtained synthetically #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: 1.87 Å3/Da / Density % sol: 34 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, CACODYLATE, MGCL2, SPERMINE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 17, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→10 Å / Num. all: 5962 / Num. obs: 5929 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 43.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 11.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: SHELXL SWAT OPTION | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 460 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 5900 / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.061 |