+Open data
-Basic information
Entry | Database: PDB / ID: 1d13 | ||||||||||||||||||
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Title | MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Frederick, C.A. / Quigley, G.J. / Teng, M.-K. / Coll, M. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J. | Citation | Journal: Eur.J.Biochem. / Year: 1989 | Title: Molecular structure of an A-DNA decamer d(ACCGGCCGGT). Authors: Frederick, C.A. / Quigley, G.J. / Teng, M.K. / Coll, M. / Van der Marel, G.A. / Van Boom, J.H. / Rich, 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 | 1d13.cif.gz | 16.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d13.ent.gz | 9.1 KB | Display | PDB format |
PDBx/mmJSON format | 1d13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d13_validation.pdf.gz | 319.7 KB | Display | wwPDB validaton report |
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Full document | 1d13_full_validation.pdf.gz | 332.6 KB | Display | |
Data in XML | 1d13_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1d13_validation.cif.gz | 3.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d13 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d13 | 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: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.76 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / Details: VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Detector | Type: NICOLET P3 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. all: 4200 / Num. obs: 1434 / Observed criterion σ(F): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→20 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Num. reflection obs: 1434 / Rfactor obs: 0.18 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.026 |