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Yorodumi- PDB-1m6r: Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6r | ||||||||||||||||||
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Title | Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang | ||||||||||||||||||
Components | 5'-R(*Keywords | DNA / Z-DNA / overhang | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | Authors | Pan, B. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 | Title: Crystal structure of rGd(CGCGCG): a Z-DNA hexamer duplex with a 5'-(rG) overhang. Authors: Pan, B. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m6r.cif.gz | 14.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m6r.ent.gz | 9.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m6r_validation.pdf.gz | 366.2 KB | Display | wwPDB validaton report |
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Full document | 1m6r_full_validation.pdf.gz | 366.2 KB | Display | |
Data in XML | 1m6r_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 1m6r_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6r ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6r | HTTPS FTP |
-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
#1: DNA chain | Mass: 2139.411 Da / Num. of mol.: 2 / Source method: obtained synthetically #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 grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2-propanol (at reservoir), Spermine tetrachloride, magnesium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
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 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 8, 1997 / Details: mirrors |
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: 1.54→29 Å / Num. obs: 3576 / % possible obs: 87.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049 |
Reflection shell | Resolution: 1.54→1.65 Å / Rmerge(I) obs: 0.195 / % possible all: 79.9 |
Reflection | *PLUS Num. measured all: 12118 |
Reflection shell | *PLUS % possible obs: 79.9 % |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | |||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→8 Å / Isotropic thermal model: isotropic / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.54→8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 3536 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.191 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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