+Open data
-Basic information
Entry | Database: PDB / ID: 1zf5 | ||||||||||||||||||
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Title | GCT 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 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 | 1zf5.cif.gz | 14.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zf5.ent.gz | 8.4 KB | Display | PDB format |
PDBx/mmJSON format | 1zf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zf5_validation.pdf.gz | 380.9 KB | Display | wwPDB validaton report |
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Full document | 1zf5_full_validation.pdf.gz | 381.6 KB | Display | |
Data in XML | 1zf5_validation.xml.gz | 2 KB | Display | |
Data in CIF | 1zf5_validation.cif.gz | 2.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/1zf5 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/1zf5 | HTTPS FTP |
-Related structure data
Related structure data | 1zewC 1zexC 1zeyC 1zezC 1zf0C 1zf1C 1zf2C 1zf3C 1zf4C 1zf6C 1zf7C 1zf8C 1zf9C 1zfaC 1zfbC 1zfcC 1zfeC 1zffC 1zfgC 1zfhC 1zfmC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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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: 3045.992 Da / Num. of mol.: 1 / 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. |
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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: 2.04 Å3/Da / Density % sol: 39.62 % | ||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→11.07 Å / Num. obs: 12303 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 0.7 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 0.99→1.03 Å / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.161 / % possible all: 43.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.99→11.07 Å / Cor.coef. Fo:Fc: 0.825 / Cor.coef. Fo:Fc free: 0.849 / SU B: 0.529 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: STRUCTURE IS NOT REFINED TO ITS LOWEST R VALUES, REFER TO CITATION. ALTERNATE CONFORMATIONS CLEARLY VISIBLE ALONG DNA BACKBONE.`
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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: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: -0.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→11.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.99→1.05 Å / Total num. of bins used: 6
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