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- PDB-2hbn: Crystallization of the Tl+-form of the Oxytricha nova G-quadruplex -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hbn | ||||||||||||||||||
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Title | Crystallization of the Tl+-form of the Oxytricha nova G-quadruplex | ||||||||||||||||||
![]() | 5'-D(*![]() ![]() ![]() ![]() ![]() Function / homology | THALLIUM (I) ION / | ![]() ![]() Method | ![]() ![]() ![]() ![]() Gill, M.L. / Strobel, S.A. / Loria, J.P. | ![]() ![]() Title: Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex. Authors: Gill, M.L. / Strobel, S.A. / Loria, J.P. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.6 KB | Display | ![]() |
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PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jrnS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: This sequence occurs naturally in Sterkiella nova telomere #2: Chemical | ChemComp-TL / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.03 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.5 mM DNA, 50 mM Potassium cacodylate, 10 mM Magnesium acetate, 40 mM Potassium acetate, 5% (v/v) MPD mixed with equal amount of 35% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2005 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→43.11 Å / Num. all: 19237 / Num. obs: 18241 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.187 / Χ2: 0.908 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 1 / Num. unique all: 3522 / Χ2: 0.561 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1JRN Resolution: 1.55→43.11 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.774 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→43.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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