+Open data
-Basic information
Entry | Database: PDB / ID: 1zfm | ||||||||||||||||||
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Title | AGC Duplex B-DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | Authors | Hays, F.A. / Teegarden, A.T. / Jones, Z.J.R. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S. | Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 | Title: How sequence defines structure: a crystallographic map of DNA structure and conformation. Authors: Hays, F.A. / Teegarden, A. / Jones, Z.J. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zfm.cif.gz | 25.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zfm.ent.gz | 14.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/1zfm ftp://data.pdbj.org/pub/pdb/validation_reports/zf/1zfm | HTTPS FTP |
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-Related structure data
Related structure data | 1zewC 1zexC 1zeyC 1zezC 1zf0C 1zf1C 1zf2C 1zf3C 1zf4C 1zf5C 1zf6C 1zf7C 1zf8C 1zf9C 1zfaC 1zfbC 1zfcC 1zfeC 1zffC 1zfgC 1zfhC C: citing same article (ref.) |
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Similar 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: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY ...Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. #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: 2.17 Å3/Da / Density % sol: 43.3 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 7 Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. obs: 2577 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 4 / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NDB ENTRY BD0028 Resolution: 2.2→17.11 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.668 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.589 / ESU R Free: 0.369 / Stereochemistry target values: MAWIMUM LIKELIHOOD Details: STRUCTURE IS NOT FULLY REFINED. REPEA BD0028 FROM SAME LAB. WILL BE UPDATED AS BETTER DATA IS OBTAINE TO CITATION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→17.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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