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Yorodumi- PDB-4lth: Dehydration/Rehydration of a Nucleic Acid system containing a Pol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lth | ||||||
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Title | Dehydration/Rehydration of a Nucleic Acid system containing a Polypyridyl Ruthenium Complex at 97% relative humidity (3/7) | ||||||
Components | DNA | ||||||
Keywords | DNA / Dehydration / HC1b / Kinking / ruthenium | ||||||
Function / homology | : / Ru(tap)2(dppz) complex / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Hall, J.P. / Sanchez-Weatherby, J. / Cardin, C.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Controlled Dehydration of a Ruthenium Complex-DNA Crystal Induces Reversible DNA Kinking. Authors: Hall, J.P. / Sanchez-Weatherby, J. / Alberti, C. / Quimper, C.H. / O'Sullivan, K. / Brazier, J.A. / Winter, G. / Sorensen, T. / Kelly, J.M. / Cardin, D.J. / Cardin, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lth.cif.gz | 19.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lth.ent.gz | 11.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lth_validation.pdf.gz | 758.1 KB | Display | wwPDB validaton report |
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Full document | 4lth_full_validation.pdf.gz | 760 KB | Display | |
Data in XML | 4lth_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 4lth_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/4lth ftp://data.pdbj.org/pub/pdb/validation_reports/lt/4lth | HTTPS FTP |
-Related structure data
Related structure data | 4ltfC 4ltgC 4ltiC 4ltjC 4ltkC 4ltlC 3qrnS S: Starting model for refinement 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: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesised by ATDBio |
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#2: Chemical | ChemComp-RKL / |
#3: Chemical | ChemComp-BA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 1ul 1mM d(TCGGCGCCGA)2, 1ul 4mM lambda-[Ru(TAP)2(dppz)]2+, 6ul 12mM spermine, 10% MPD, 40mM sodium cacodylate, 80mM KCl, 20mM BaCl2. Equilibriated against 1ml 35% MPD. Crystal was rehydrated ...Details: 1ul 1mM d(TCGGCGCCGA)2, 1ul 4mM lambda-[Ru(TAP)2(dppz)]2+, 6ul 12mM spermine, 10% MPD, 40mM sodium cacodylate, 80mM KCl, 20mM BaCl2. Equilibriated against 1ml 35% MPD. Crystal was rehydrated to 97% relative humidity on the beamline using the HC1b., pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8266 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2012 |
Radiation | Monochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30.39 Å / Num. all: 4564 / Num. obs: 4564 / % possible obs: 88.6 % / Observed criterion σ(I): 2.7 |
Reflection shell | Resolution: 1.6→1.64 Å / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QRN Resolution: 1.6→30.39 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.408 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 29.108 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30.39 Å
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Refine LS restraints |
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