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Open data
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Basic information
Entry | Database: PDB / ID: 1jrn | ||||||||||||||||||
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Title | Orthorhombic form of Oxytricha telomeric DNA at 2.0A | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / oxytricha / G-quartets | Function / homology | : / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Haider, S.M. / Parkinson, G. / Neidle, S. | ![]() ![]() Title: Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. Authors: Haider, S. / Parkinson, G.N. / Neidle, S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.8 KB | Display | ![]() |
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PDB format | ![]() | 31 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394 KB | Display | ![]() |
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Full document | ![]() | 395 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 9.7 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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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 IS THE OXYTRICHA NOVA TELOMERIC SEQUENCE #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.18 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, Potassium Chloride, Magnesium Chloride, Spermine, Cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 12 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 10, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 8736 / Num. obs: 8565 / % possible obs: 98 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.052 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.84 / % possible all: 98.2 |
Reflection | *PLUS Lowest resolution: 8 Å / % possible obs: 98 % / Redundancy: 2.08 % / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 98.2 % / Rmerge(I) obs: 0.19 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor all: 0.2753 / Rfactor obs: 0.262 / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.215 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |