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Yorodumi- PDB-1d90: REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH I.T MI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d90 | ||||||||||||||||||
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Title | REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH I.T MISMATCHED BASE PAIRS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | Authors | Cruse, W.B.T. / Aymani, J. / Kennard, O. / Brown, T. / Jack, A.G.C. / Leonard, G.A. | Citation | Journal: Nucleic Acids Res. / Year: 1989 | Title: Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs. Authors: Cruse, W.B. / Aymani, J. / Kennard, O. / Brown, T. / Jack, A.G. / Leonard, G.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d90.cif.gz | 19.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d90.ent.gz | 11.5 KB | Display | PDB format |
PDBx/mmJSON format | 1d90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d90_validation.pdf.gz | 319 KB | Display | wwPDB validaton report |
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Full document | 1d90_full_validation.pdf.gz | 337.8 KB | Display | |
Data in XML | 1d90_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 1d90_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d90 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d90 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2428.590 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.21 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 / Method: other | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Detector | Type: SIEMENS AED2 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.66 Å / Num. all: 5795 / Num. obs: 3310 / % possible obs: 57 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.04 |
Reflection | *PLUS Observed criterion σ(F): 1 / Rmerge(I) obs: 0.04 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Highest resolution: 1.7 Å / σ(F): 2 /
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Refine Biso | Class: ALL ATOMS / Details: TR / Treatment: isotropic | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 2 / Num. reflection obs: 2853 / Rfactor obs: 0.14 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |