+Open data
-Basic information
Entry | Database: PDB / ID: 6gds | ||||||
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Title | Holliday Junctions formed from Telomeric DNA | ||||||
Components |
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Keywords | RECOMBINATION / Holliday junction / Homologous recombination / Telomeres / ALT mechanism / ACC structural motif. | ||||||
Function / homology | DNA Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 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 | 6gds.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gds.ent.gz | 20.2 KB | Display | PDB format |
PDBx/mmJSON format | 6gds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gds_validation.pdf.gz | 378.1 KB | Display | wwPDB validaton report |
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Full document | 6gds_full_validation.pdf.gz | 378.1 KB | Display | |
Data in XML | 6gds_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 6gds_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/6gds ftp://data.pdbj.org/pub/pdb/validation_reports/gd/6gds | HTTPS FTP |
-Related structure data
Related structure data | 6gdhC 6gdnC 3hs1S 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: 2972.982 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: DNA chain | Mass: 3115.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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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: 2.42 Å3/Da / Density % sol: 49.22 % / Description: Small hexagonal plates |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25 mM Potassium Chloride, 10 mM Potassium Cacodylate, 50mM Magnesium Chloride, 20mM Calcium Chloride, 35% 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: I24 / Wavelength: 0.92016 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2015 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92016 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→15.74 Å / Num. obs: 2615 / % possible obs: 92.9 % / Redundancy: 1.8 % / CC1/2: 0.947 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.114 / Rrim(I) all: 0.161 / Net I/σ(I): 5.6 | ||||||||||||||||||||||||||||||
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: 3HS1 Resolution: 2.95→15.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 20.494 / SU ML: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.551 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: 72.563 Å2 / Biso min: 35.58 Å2
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Refinement step | Cycle: final / Resolution: 2.95→15.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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