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Yorodumi- PDB-1d7z: CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 2.2 A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d7z | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 2.2 A RESOLUTION | ||||||||||||||||||
Components | 5'-H(*Keywords | DNA / HEXITOL NUCLEIC ACID / DNA ANALOGUE / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.21 Å | Authors | Declercq, R. / Van Meervelt, L. | Citation | Journal: J.Am.Chem.Soc. / Year: 2002 Title: Crystal structure of double helical hexitol nucleic acids. Authors: Declercq, R. / Van Aerschot, A. / Read, R.J. / Herdewijn, P. / Van Meervelt, L. #1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1995 Title: 1',5'-Anhydrohexitol nucleic acids, a new promising antisense construct Authors: Van Aerschot, A. / Verheggen, I. / Hendrix, C. / Herdewijn, P. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: 1',5'-anhydro-2',3'-dideoxy-2'-(guanin-9-yl)-D-arabino-hexitol Authors: Declercq, R. / Herdewijn, P. / Van Meervelt, L. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Oligonucleotides with 1',5'-anhydrohexitol nucleoside building blocks: Crystallization and preliminary X-ray studies of H(GTGTACAC) Authors: Declercq, R. / Van Aerschot, A. / Herdewijn, P. / Van Meervelt, L. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d7z.cif.gz | 15 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d7z.ent.gz | 10.1 KB | Display | PDB format |
PDBx/mmJSON format | 1d7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d7z ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d7z | HTTPS FTP |
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-Related structure data
Related structure data | 481dC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 2538.831 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE MOLECULE WAS CHEMICALLY SYNTESISED (SEE REFERENCE 1) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CACODYLATE BUFFER, KCL, BACL2, SPERMINE TETRACHLORIDE AND MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→20 Å / Num. all: 1344 / Num. obs: 1344 / % possible obs: 83.8 % / Observed criterion σ(I): 0 / Redundancy: 16.8 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 2.21→2.25 Å / Rmerge(I) obs: 0.168 / % possible all: 74.1 |
Reflection | *PLUS Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 74.1 % / Rmerge(I) obs: 0.168 |
-Processing
Software |
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Refinement | Resolution: 2.21→20 Å / Cross valid method: NONE USED / σ(F): 0 / σ(I): 0 Stereochemistry target values: BASES: TAYLOR AND KENNARD VALUES; THE REST: VALUES BASED ON SINGLE CRYSTAL STRUCTURE OF HNA BUILDING BLOCKS
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Refinement step | Cycle: LAST / Resolution: 2.21→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor all: 0.233 / Rfactor obs: 0.233 / Rfactor Rwork: 0.232 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |