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Yorodumi- PDB-1enn: SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1enn | |||||||||||||||||||||
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Title | SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION | |||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / ATOMIC RESOLUTION / IONS / HYDRATION / BASE TRIPLET | Function / homology | OXYGEN ATOM / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.89 Å | Authors | Soler-Lopez, M. / Malinina, L. / Subirana, J.A. | Citation | Journal: J.Biol.Chem. / Year: 2000 | Title: Solvent organization in an oligonucleotide crystal. The structure of d(GCGAATTCG)2 at atomic resolution. Authors: Soler-Lopez, M. / Malinina, L. / Subirana, J.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1enn.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1enn.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 1enn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1enn ftp://data.pdbj.org/pub/pdb/validation_reports/en/1enn | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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
#1: DNA chain | Mass: 2755.823 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 1.84 Å3/Da / Density % sol: 33.24 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.1 Details: ACRIDINE-(ARG)4 ADDUCT, CACODYLATE, MGCL2, MPD, pH 7.1, vapor diffusion at 293K, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→30 Å / Num. all: 320317 / Num. obs: 32684 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 0.89→0.9 Å / Redundancy: 1.43 % / Rmerge(I) obs: 0.3 / % possible all: 59 |
Reflection shell | *PLUS % possible obs: 59 % |
-Processing
Software |
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Refinement | Resolution: 0.89→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: 'OXYGEN ATOMS' 179, 180, 181 REPRESENT ADDITIONAL PEAKS OF ELECTRON DENSITY FOUND AT DISTANCES 0.9-1.4 A FROM EITHER ATOM OF THE PHOSPHATE GROUPS 9, 12, 14. MOST LIKELY, THESE THREE ...Details: 'OXYGEN ATOMS' 179, 180, 181 REPRESENT ADDITIONAL PEAKS OF ELECTRON DENSITY FOUND AT DISTANCES 0.9-1.4 A FROM EITHER ATOM OF THE PHOSPHATE GROUPS 9, 12, 14. MOST LIKELY, THESE THREE 'OXYGENS' ARE A SIGN OF DISORDER OF THESE PHOSPHATES AND WERE REFINED AS OXYGEN ATOMS.
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Refinement step | Cycle: LAST / Resolution: 0.89→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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