+Open data
-Basic information
Entry | Database: PDB / ID: 2avj | ||||||||||||||||||
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Title | G4(Br)UTTG4 dimeric quadruplex | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / quadruplex / loop | Function / homology | CACODYLATE ION / : / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å | Authors | Hazel, P. / Parkinson, G.N. / Neidle, S. | Citation | Journal: J.Am.Chem.Soc. / Year: 2006 | Title: Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex. Authors: Hazel, P. / Parkinson, G.N. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2avj.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2avj.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 2avj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2avj_validation.pdf.gz | 413.3 KB | Display | wwPDB validaton report |
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Full document | 2avj_full_validation.pdf.gz | 418.4 KB | Display | |
Data in XML | 2avj_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 2avj_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/2avj ftp://data.pdbj.org/pub/pdb/validation_reports/av/2avj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3566.137 Da / Num. of mol.: 6 / Source method: obtained synthetically #2: Chemical | ChemComp-K / #3: Chemical | #4: 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: 2.11 Å3/Da / Density % sol: 37.03 % Description: The structure factor file contains Friedel pairs. | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293.15 K / Method: under oil evaporation / pH: 6.5 Details: sodium iodide, sodium cacodylate, PEG 400, pH 6.5, under oil evaporation, temperature 293.15K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9199 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.46 Å / Num. all: 6534 / Num. obs: 6534 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.032 / Χ2: 1.911 |
Reflection shell | Resolution: 2.2→2.49 Å / % possible obs: 89.5 % / Rmerge(I) obs: 0.062 / Num. measured obs: 1103 / Χ2: 1.487 / % possible all: 89.5 |
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.39→24.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.288 / WRfactor Rwork: 0.2 / SU B: 9.033 / SU ML: 0.217 / σ(F): 0 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used for phasing.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.433 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→24.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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