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Open data
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Basic information
Entry | Database: PDB / ID: 4r4d | ||||||||||||||||||||
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Title | Racemic crystal structure of a magnesium-bound B-DNA duplex | ||||||||||||||||||||
![]() | 5'-D(*![]() DNA / racemic DNA / racemates | Function / homology | DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | ![]() ![]() Title: Racemic DNA crystallography. Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.9 KB | Display | ![]() |
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PDB format | ![]() | 50.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 403.6 KB | Display | ![]() |
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Full document | ![]() | 405.9 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r44C ![]() 4r45C ![]() 4r47C ![]() 4r48C ![]() 4r49C ![]() 4r4aC ![]() 3r86S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: B-DNA duplex / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 mM DNA, 50 mM sodium cacodylate, 200 mM magnesium chloride, 2.5 mM spermine, 30% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014 |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→43.54 Å / Num. all: 42395 / Num. obs: 38749 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 47.68 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 14.11 |
Reflection shell | Resolution: 1.29→1.37 Å / % possible all: 86.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3R86 Resolution: 1.29→43.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.747 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.519 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→43.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.29→1.326 Å / Total num. of bins used: 20
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