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Open data
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Basic information
Entry | Database: PDB / ID: 6tzq | ||||||||||||||||||||||||||||
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Title | A DNA G-quadruplex/i-motif hybrid | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / G-quadruplex / i-motif / quadruplex / hybrid / non-duplex / 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 | ![]() | 23.3 KB | Display | ![]() |
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PDB format | ![]() | 13.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 247.6 KB | Display | ![]() |
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Full document | ![]() | 247.5 KB | Display | |
Data in XML | ![]() | 1013 B | Display | |
Data in CIF | ![]() | 1.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tzrSC ![]() 6tzsC S: Starting model for refinement C: citing same article ( |
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Similar 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: 3343.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-BA / | #3: 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: 2.98 Å3/Da / Density % sol: 58.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 30% PEG 400, 20 mM barium chloride, 10 mM spermidine, 30 mM Bis-Tris pH 8.5; Equilibrated against 5% PEG 400 and 4 ul of glacial acetic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.29→49.33 Å / Num. obs: 3955 / % possible obs: 99.9 % / Redundancy: 17.4 % / CC1/2: 1 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.035 / Rrim(I) all: 0.142 / Net I/σ(I): 8.2 / Num. measured all: 68659 / Scaling rejects: 117 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TZR Resolution: 2.29→32.88 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.99 / SU B: 11.591 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.42 Å2 / Biso mean: 71.434 Å2 / Biso min: 52.42 Å2
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Refinement step | Cycle: final / Resolution: 2.29→32.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.346 Å / Rfactor Rfree error: 0
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