+Open data
-Basic information
Entry | Database: PDB / ID: 1nvy | ||||||
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Title | Strontium bound to the Holliday junction sequence d(TCGGTACCGA)4 | ||||||
Components | d(TCGGTACCGA)4 | ||||||
Keywords | DNA / Holliday Junction / Strontium / Sr2+ | ||||||
Function / homology | STRONTIUM ION / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Cardin, C.J. / Thorpe, J.H. / Gale, B.C. / Teixeira, S.C.M. | ||||||
Citation | Journal: To be published Title: Strontium, a MAD taerget for the DNA Holliday junction Authors: Cardin, C.J. / Thorpe, J.H. / Gale, B.C. / Teixeira, S.C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nvy.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nvy.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nvy_validation.pdf.gz | 381.5 KB | Display | wwPDB validaton report |
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Full document | 1nvy_full_validation.pdf.gz | 386.7 KB | Display | |
Data in XML | 1nvy_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 1nvy_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/1nvy ftp://data.pdbj.org/pub/pdb/validation_reports/nv/1nvy | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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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: Chemically synthezied #2: Chemical | ChemComp-SR / #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: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: SrCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9470, 0.7301, 0.7667, 0.7670 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 2002 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→20 Å / Num. all: 16734 / Num. obs: 16734 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 20.89 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.58 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.88 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.38 / Num. unique all: 2509 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→34.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.973 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.1 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.039 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→34.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.581 Å / Total num. of bins used: 10 /
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