+Open data
-Basic information
Entry | Database: PDB / ID: 1dc0 | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / B-DNA / INTERMEDIATE | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS BASED ON THE IODINATED SEQUENCE D(CAT(IODO-G)GGCCCATG) / Resolution: 1.3 Å | Authors | Ng, H.L. / Kopka, M.L. / Dickerson, R.E. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 | Title: The structure of a stable intermediate in the A ;-> B DNA helix transition Authors: Ng, H.L. / Kopka, M.L. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dc0.cif.gz | 34.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dc0.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dc0 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dc0 | 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
#1: DNA chain | Mass: 3663.392 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 | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.3MM DUPLEX DNA, 120 MM CALCIUM ACETATE, 4.8 MM SPERMINE, 60 MM SODIUM CACODYLATE BUFFER, PH 7.0, 9.5% MPD IN DROP, 25% MPD IN RESERVOIR, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 0.978 |
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→25 Å / Num. all: 16190 / Num. obs: 16190 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 43.6 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.179 / % possible all: 91.2 |
Reflection | *PLUS Num. obs: 16111 / % possible obs: 98.6 % / Num. measured all: 128129 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 7.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS BASED ON THE IODINATED SEQUENCE D(CAT(IODO-G)GGCCCATG) Resolution: 1.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |