+Open data
-Basic information
Entry | Database: PDB / ID: 4okl | ||||||
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Title | Crystal Structure of d(CCCCGGTACCGGGG)2 at 1.65 Angstrom | ||||||
Components | 14 mer A-DNA | ||||||
Keywords | DNA / A-DNA / Tetra-decanucleotide / Crystal packing / Right handed / double helix | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Anna, V. / Monica, P. / Mandal, P.K. / Gautham, N. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Structure of d(CCCCGGTACCGGGG)2 at 1.65 angstrom resolution. Authors: Purushothaman, M. / Varghese, A. / Mandal, P.K. / Gautham, N. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 2011 Title: The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)2. Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N. #2: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex. Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4okl.cif.gz | 39.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4okl.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 4okl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/4okl ftp://data.pdbj.org/pub/pdb/validation_reports/ok/4okl | HTTPS FTP |
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-Related structure data
Related structure data | 3v9dS 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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Unit cell |
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-Components
#1: DNA chain | Mass: 4282.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized oligo nucleotide fragment. #2: 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: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM DNA, 50mM Sodium Cacodylate buffer, 10mM ZnCl2, 10mM Spermine, 33% MPD (v/v), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 |
Radiation | Monochromator: SI (111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30.05 Å / Num. all: 9714 / Num. obs: 9714 / % possible obs: 100 % / Observed criterion σ(F): 1.65 / Observed criterion σ(I): 1.65 / Redundancy: 13.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 1357 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.141 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3V9D Resolution: 1.65→30.048 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 26.57 / 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: 1.65→30.048 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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