+Open data
-Basic information
Entry | Database: PDB / ID: 3gom | ||||||||||||||||||
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Title | Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Holliday junction structure | Function / homology | : / DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | Authors | Naseer, A. / Cardin, C.J. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 | Title: Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand. Authors: Hall, J.P. / O'Sullivan, K. / Naseer, A. / Smith, J.A. / Kelly, J.M. / 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 | 3gom.cif.gz | 21.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gom.ent.gz | 13.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gom_validation.pdf.gz | 382.2 KB | Display | wwPDB validaton report |
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Full document | 3gom_full_validation.pdf.gz | 382.2 KB | Display | |
Data in XML | 3gom_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 3gom_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/3gom ftp://data.pdbj.org/pub/pdb/validation_reports/go/3gom | HTTPS FTP |
-Related structure data
Related structure data | 3qf8C 3qrnC 1nvyS 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.: 2 / Source method: obtained synthetically / Details: Holliday junction structure #2: Chemical | ChemComp-BA / #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: 2.24 Å3/Da / Density % sol: 45.05 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: BaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å |
Detector | Type: OXFORD SAPPHIRE CCD / Detector: CCD / Details: multigraded optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.956 Å / Num. all: 2518 / Num. obs: 2351 / % possible obs: 93.22 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 31.247 Å2 / Limit h max: 26 / Limit h min: -28 / Limit k max: 10 / Limit k min: 0 / Limit l max: 16 / Limit l min: 0 / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.21 / Num. unique all: 461 / % possible all: 93.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NVY Resolution: 2.3→19.956 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.86 / SU B: 13.5 / SU ML: 0.291 / SU R Cruickshank DPI: 0.604 / Cross valid method: THROUGHOUT / ESU R Free: 0.371
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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: 31.247 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.956 Å
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Refine LS restraints |
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