+Open data
-Basic information
Entry | Database: PDB / ID: 4r44 | ||||||||||||||||||||
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Title | Racemic crystal structure of a tetramolecular DNA G-quadruplex | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / racemic DNA / racemates | Function / homology | : / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.695 Å | Authors | Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r44.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r44.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 4r44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r44_validation.pdf.gz | 419.9 KB | Display | wwPDB validaton report |
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Full document | 4r44_full_validation.pdf.gz | 420.8 KB | Display | |
Data in XML | 4r44_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 4r44_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r44 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r44 | HTTPS FTP |
-Related structure data
Related structure data | 4r45C 4r47C 4r48C 4r49C 4r4aC 4r4dC 352dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 1880.251 Da / Num. of mol.: 16 / Source method: obtained synthetically / Details: Tetramolecular G-Quadruplex / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-NA / #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: 2.01 Å3/Da / Density % sol: 38.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 1 mM DNA, 50 mM potassium cacodylate, 40 mM potassium chloride, 100 mM magnesium chloride hexahydrate, 1.7 M 1,6-hexanediol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 26, 2013 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.695→37.886 Å / Num. all: 12894 / Num. obs: 12597 / % possible obs: 97.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 49.77 Å2 / Rmerge(I) obs: 0.1643 / Net I/σ(I): 1.7 |
Reflection shell | Resolution: 2.695→2.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4338 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1292 / % possible all: 97.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 352D Resolution: 2.695→37.886 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.219 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 27.827 Å2
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Refinement step | Cycle: LAST / Resolution: 2.695→37.886 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.695→2.765 Å / Total num. of bins used: 20
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