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Yorodumi- PDB-1ehv: A NEW CRYSTAL STRUCTURE FOR THE DODECAMER C-G-C-G-A-A-T-T-C-G-C-G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ehv | ||||||||||||||||||
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Title | A NEW CRYSTAL STRUCTURE FOR THE DODECAMER C-G-C-G-A-A-T-T-C-G-C-G: SYMMETRY EFFECTS ON SEQUENCE-DEPENDENT DNA STRUCTURE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / DICKERSON DODECAMER / CRYSTAL PACKING | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | Authors | Johansson, E.M. | Citation | Journal: J.Mol.Biol. / Year: 2000 | Title: A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure. Authors: Johansson, E. / Parkinson, G. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ehv.cif.gz | 16.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ehv.ent.gz | 9.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ehv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ehv_validation.pdf.gz | 356.7 KB | Display | wwPDB validaton report |
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Full document | 1ehv_full_validation.pdf.gz | 358.2 KB | Display | |
Data in XML | 1ehv_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1ehv_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1ehv ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1ehv | 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3663.392 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: KCL, BACL2, MPD, SPERMINE TETRAHYDROCHLORIDE, SODIUM CACODYLATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 284K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 284 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 3916 / Num. obs: 2685 / % possible obs: 68.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.206 / % possible all: 0.62 |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL.
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.301 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |