+Open data
-Basic information
Entry | Database: PDB / ID: 325d | ||||||||||||||||||
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Title | CRYSTAL STRUCTURES OF D(CM5CGGGCCM5CGG)-HEXAGONAL FORM | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | Authors | Tippin, D.B. / Sundaralingam, M. | Citation | Journal: J.Mol.Biol. / Year: 1997 | Title: Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on ...Title: Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA. Authors: Tippin, D.B. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 325d.cif.gz | 21.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb325d.ent.gz | 14.6 KB | Display | PDB format |
PDBx/mmJSON format | 325d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 325d_validation.pdf.gz | 368.4 KB | Display | wwPDB validaton report |
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Full document | 325d_full_validation.pdf.gz | 372.8 KB | Display | |
Data in XML | 325d_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 325d_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/25/325d ftp://data.pdbj.org/pub/pdb/validation_reports/25/325d | HTTPS FTP |
-Related structure data
Related structure data | 318dC 319dC 320dC 321dC 322dC 323dC 324dC 326dC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3075.035 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: 3.22 Å3/Da / Density % sol: 61.79 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 2557 / % possible obs: 74 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0498 / Net I/σ(I): 12.2 |
Reflection | *PLUS Num. all: 2642 / % possible obs: 74 % |
-Processing
Software |
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Refinement | Resolution: 2.5→8 Å / σ(F): 1
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |