+Open data
-Basic information
Entry | Database: PDB / ID: 1s23 | ||||||||||||||||||
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Title | Crystal Structure Analysis of the B-DNA Decamer CGCAATTGCG | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / deoxyoligonucleotide / cobalt / variability | Function / homology | : / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Valls, N. / Wright, G. / Steiner, R.A. / Murshudov, G.N. / Subirana, J.A. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 | Title: DNA variability in five crystal structures of d(CGCAATTGCG). Authors: Valls, N. / Wright, G. / Steiner, R.A. / Murshudov, G.N. / Subirana, J.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s23.cif.gz | 16.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s23.ent.gz | 10.1 KB | Display | PDB format |
PDBx/mmJSON format | 1s23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/1s23 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/1s23 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.65 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, acridine(RGR), cacodylate, calcium chloride, cobalt chloride, spermine , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.917 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. obs: 4174 / % possible obs: 98.4 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.061 / Rsym value: 0.077 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.93 / Num. unique all: 376 / Rsym value: 0.6 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NDB ENTRY UDJ031 Resolution: 1.6→22.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.747 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.833 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→22.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.644 Å / Total num. of bins used: 20 /
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