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Yorodumi- PDB-1r3z: Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effect... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r3z | ||||||||||||||||||
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Title | Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effects of methylation on alternating DNA octamers | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Molecular Placement / Resolution: 1.7 Å | Authors | Shi, K. / Pan, B. / Tippin, D. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 | Title: Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers. Authors: Shi, K. / Pan, B. / Tippin, D. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r3z.cif.gz | 12.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r3z.ent.gz | 8.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/1r3z ftp://data.pdbj.org/pub/pdb/validation_reports/r3/1r3z | HTTPS FTP |
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-Related 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: 2456.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Synthesizer |
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#2: 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: 2.25 Å3/Da / Density % sol: 45.43 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: cacodylate, magnesium chloride, spermine tetrachloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→10 Å / Num. all: 2799 / Num. obs: 2540 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 1.7 Å / % possible all: 90.7 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 2711 / % possible obs: 90 % / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 80.5 % / Rmerge(I) obs: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular Placement / Resolution: 1.7→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.193 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.313 / Rfactor Rwork: 0.262 |