+Open data
-Basic information
Entry | Database: PDB / ID: 1dnx | ||||||||||||||||||
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Title | RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES | ||||||||||||||||||
Components | DNA/RNA (5'-R(*Keywords | DNA-RNA HYBRID / DNA CONFORMATION / RNA/DNA HYBRID / METAL IONS / DNA-RNA COMPLEX | Function / homology | DNA/RNA hybrid | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | Authors | Robinson, H. / Gao, Y.-G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J. | Citation | Journal: Nucleic Acids Res. / Year: 2000 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dnx.cif.gz | 22.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dnx.ent.gz | 14.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dnx_validation.pdf.gz | 366.4 KB | Display | wwPDB validaton report |
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Full document | 1dnx_full_validation.pdf.gz | 367.1 KB | Display | |
Data in XML | 1dnx_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1dnx_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/1dnx ftp://data.pdbj.org/pub/pdb/validation_reports/dn/1dnx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA/RNA hybrid | Mass: 3061.005 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 22, 1999 |
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→20 Å / Num. all: 5659 / Num. obs: 5659 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 47.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 17.7 / % possible all: 94 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Resolution: 1.7→20 Å / Num. parameters: 1979 / Num. restraintsaints: 1758 / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 / Stereochemistry target values: G.PARKINSON ET AL.
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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: 491 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.194 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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