+Open data
-Basic information
Entry | Database: PDB / ID: 3gnk | ||||||||||||||||||
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Title | Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Holliday junction Calcium ion Ca2+ | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | Authors | Naseer, A. / Cardin, C.J. | Citation | Journal: To be Published | Title: Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4 Authors: Naseer, A. / 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 | 3gnk.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gnk.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gnk_validation.pdf.gz | 390.7 KB | Display | wwPDB validaton report |
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Full document | 3gnk_full_validation.pdf.gz | 390.8 KB | Display | |
Data in XML | 3gnk_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 3gnk_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnk ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnk | HTTPS FTP |
-Related structure data
Related structure data | 1l4jS S: Starting model for refinement |
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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: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Holliday junctions #2: Chemical | #3: Chemical | #4: 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: 2.27 Å3/Da / Density % sol: 45.73 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: CaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K, temperature 290.0K | ||||||||||||||||||||||||||||
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: multilayer 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: 2.1→16.347 Å / Num. all: 6643 / Num. obs: 6622 / % possible obs: 99.41 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 17.122 Å2 / Limit h max: 29 / Limit h min: -31 / Limit k max: 11 / Limit k min: 0 / Limit l max: 35 / Limit l min: 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.44 |
Reflection scale | Group code: 1 |
Reflection shell | Resolution: 2.1→2.155 Å / Redundancy: 3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 2.35 / Num. unique all: 1773 / % possible all: 99.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1L4J Resolution: 2.1→16.347 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.862 / SU ML: 0.158 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.26
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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: 17.122 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→16.347 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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