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Open data
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Basic information
Entry | Database: PDB / ID: 4z4b | ||||||||||||||||||||
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Title | 2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Hoechst | Function / homology | Chem-4L1 / DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Wee, J.-Y. / Dobson, R.C.J. / White, J.M. | ![]() ![]() Title: 2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector Authors: Wee, J.-Y. / Dobson, R.C.J. / White, J.M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.1 KB | Display | ![]() |
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PDB format | ![]() | 23.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-4L1 / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The hanging drops contained the following constituents (final drop concentrations): DNA 0.63 mM, Ligand 1 0.63 mM, MgCl2 2.1 mM, spermine 1.05 mM, MPD 4.2%. MgCl2 and spermine were made in ...Details: The hanging drops contained the following constituents (final drop concentrations): DNA 0.63 mM, Ligand 1 0.63 mM, MgCl2 2.1 mM, spermine 1.05 mM, MPD 4.2%. MgCl2 and spermine were made in 30 mM sodium cacodylate buffer at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9567 Å / Relative weight: 1 |
Reflection | Resolution: 1.965→40.8 Å / Num. obs: 8900 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.965→2.01 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.1 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Unpublished model Resolution: 1.9652→34.485 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 24.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9652→34.485 Å
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Refine LS restraints |
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LS refinement shell |
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