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Yorodumi- PDB-1d78: HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d78 | ||||||||||||||||||
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Title | HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | Authors | Thota, N. / Li, X.H. / Bingman, C.A. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: High-resolution refinement of the hexagonal A-DNA octamer d(GTGTACAC) at 1.4 A. Authors: Thota, N. / Li, X.H. / Bingman, C.A. / Sundaralingam, M. #1: Journal: Biochemistry / Year: 1991 Title: Hexagonal Crystal Structure of the A-DNA Octamer d(GTGTACAC) and Its Comparison with the Tetragonal Structure: Correlated Variations in Helical Parameters Authors: Jain, S. / Zon, G. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d78.cif.gz | 11.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d78.ent.gz | 7.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d78_validation.pdf.gz | 357.1 KB | Display | wwPDB validaton report |
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Full document | 1d78_full_validation.pdf.gz | 358.7 KB | Display | |
Data in XML | 1d78_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 1d78_validation.cif.gz | 3.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d78 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d78 | HTTPS FTP |
-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: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 283.00K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 283 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 258 K |
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Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.4→5 Å / Num. all: 7730 / Num. obs: 4365 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 5 Å / Num. all: 5261 / % possible obs: 86 % / Observed criterion σ(I): 2 / Num. measured all: 9036 / Rmerge(I) obs: 0.034 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.4→5 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.4→5 Å
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 5 Å / Num. reflection obs: 7730 / σ(F): 2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |