+Open data
-Basic information
Entry | Database: PDB / ID: 6gdn | ||||||
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Title | Holliday Junctions formed from Telomeric DNA | ||||||
Components | Telomere DNA (42-MER) | ||||||
Keywords | RECOMBINATION / Holliday junction / Homologous recombination / Telomeres / ALT mechanism / ACC structural motif. | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | Parkinson, G.N. / Haider, S. / Li, P. / Khiali, S. / Munnur, D. / Ramanathan, A. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Holliday Junctions Formed from Human Telomeric DNA. Authors: Haider, S. / Li, P. / Khiali, S. / Munnur, D. / Ramanathan, A. / Parkinson, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gdn.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gdn.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 6gdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gdn_validation.pdf.gz | 379.8 KB | Display | wwPDB validaton report |
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Full document | 6gdn_full_validation.pdf.gz | 381.1 KB | Display | |
Data in XML | 6gdn_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 6gdn_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/6gdn ftp://data.pdbj.org/pub/pdb/validation_reports/gd/6gdn | HTTPS FTP |
-Related structure data
Related structure data | 6gdhC 6gdsC 6dgh 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: 12903.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Human telomeric DNA sequence / Source: (synth.) Homo sapiens (human) #2: Chemical | |
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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: 2.75 Å3/Da / Density % sol: 55.28 % / Description: Large flat hexagonal plates |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.04 M Magnesium acetate tetrahydrate, 0.05 M Sodium cacodylate trihydrate, 30% v/v (+/-)-2-Methyl-2,4-pentanediol. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2017 | ||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.68→45.38 Å / Num. obs: 8053 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DGH 6dgh Resolution: 3→45.38 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / Matrix type: sparse / SU B: 22.957 / SU ML: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.479 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120 Å2 / Biso mean: 68.308 Å2 / Biso min: 20.18 Å2
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Refinement step | Cycle: final / Resolution: 3→45.38 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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