+Open data
-Basic information
Entry | Database: PDB / ID: 1zf4 | ||||||||||||||||||
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Title | ATC Four-stranded DNA Holliday Junction | ||||||||||||||||||
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: 1.65 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 | 1zf4.cif.gz | 23.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zf4.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/1zf4 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/1zf4 | HTTPS FTP |
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-Related structure data
Related structure data | 1zewC 1zexC 1zeyC 1zezC 1zf0C 1zf1C 1zf2C 1zf3C 1zf5C 1zf6C 1zf7C 1zf8C 1zf9C 1zfaC 1zfbC 1zfcC 1zfeC 1zffC 1zfgC 1zfhC 1zfmC 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.005 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: Chemical | ChemComp-NA / | #3: 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: 2.26 Å3/Da / Density % sol: 45.67 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
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-ID-B / Wavelength: 1.072 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→12.7 Å / Num. obs: 5414 / % possible obs: 79.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055 / Rsym value: 0.054 / Χ2: 1.051 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.65→1.71 Å / % possible obs: 32.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 216 / Rsym value: 0.179 / Χ2: 0.68 / % possible all: 48.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ndb entry UD0058 Resolution: 1.65→12.7 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.788 / SU B: 5.511 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 10.578 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→12.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Label seq-ID: 1 - 10
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