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Open data
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Basic information
Entry | Database: PDB / ID: 6tzs | ||||||||||||||||||||||||||||
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Title | A DNA i-motif/duplex hybrid | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / i-motif / duplex / quadruplex / hybrid / noncanonical | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Chu, B. / Paukstelis, P.J. | Funding support | | ![]()
![]() ![]() Title: A DNA G-quadruplex/i-motif hybrid. Authors: Chu, B. / Zhang, D. / Paukstelis, P.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.2 KB | Display | ![]() |
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PDB format | ![]() | 14.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.8 KB | Display | ![]() |
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Full document | ![]() | 383.9 KB | Display | |
Data in XML | ![]() | 3.2 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 3422.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% MPD, 120 mM calcium chloride, 20 mM lithium chloride, 8 mM spermidine, 30 mM sodium cacodylate; Equilibrated against 20% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9187 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→55.8 Å / Num. obs: 2540 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.743 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.058 / Rrim(I) all: 0.182 / Net I/σ(I): 11.5 / Num. measured all: 30879 / Scaling rejects: 36 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.82 / Num. measured all: 3740 / Num. unique obs: 294 / CC1/2: 0.233 / Rpim(I) all: 0.526 / Rrim(I) all: 1.895 / Net I/σ(I) obs: 1.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.19 Å2 / Biso mean: 46.873 Å2 / Biso min: 17.39 Å2
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Refinement step | Cycle: final / Resolution: 2.6→46.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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