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Open data
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Basic information
Entry | Database: PDB / ID: 2wna | ||||||
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Title | Crystal structure of the GNA 3'-G(Br)CGCGC-2' | ||||||
![]() | GNA | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | COBALT HEXAMMINE(III) / ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schlegel, M.K. / Essen, L.-O. / Meggers, E. | ||||||
![]() | ![]() Title: Atomic Resolution Duplex Structure of the Simplified Nucleic Acid Gna. Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E. #1: ![]() Title: Duplex Structure of a Minimal Nucleic Acid. Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.4 KB | Display | ![]() |
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PDB format | ![]() | 18.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: RNA chain | Mass: 1636.884 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SYNTHETIC GLYCOL NUCLEIC ACID, 3'-(S)-((ZGU)P(ZBC)P(ZGU)P(ZCY)P(ZGU)P(ZCY))-2' Source: (synth.) ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | ![]() Nonpolymer details | (S)-1'-(2',3'-DIHYDROXYPROPYL)-5-BROMO-CYTOSINE (ZBC): ZCY ANALOG BEARING A BROMINE AT C5 COBALT ...(S)-1'-(2',3'-DIHYDROXYP | Sequence details | CYTOSINE A2 IS BROMINATED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.41 Å3/Da / Density % sol: 12.73 % Description: LOW AND HIGH RESOLUTION DATA MERGED FROM SAME CRYSTAL. DATA RECORDING OCCURED AT PEAK WAVELENGTH OF BROMINE |
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Crystal grow![]() | pH: 5.5 Details: DROP: 2 MM G(BR)CGCGC, 10% 2-METHYL-2,4-PENTANEDIOL, 40 MM SODIUM CACODYLATE (PH 5.5), 20 MM COBALT HEXAMINE, 80 MM SODIUM CHLORIDE, 20 MM MAGNESIUM CHLORIDE RESERVOIR: 35 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.96→21 Å / Num. obs: 30224 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 4.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 0.96→1.02 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.2 / % possible all: 0.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: NONE Resolution: 0.97→8 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.434 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GNA DUPLEX OF TYPE N FORMED WITH SYMMETRY- EQUIVALENT MOLECULE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.688 Å2
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Refinement step | Cycle: LAST / Resolution: 0.97→8 Å
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Refine LS restraints |
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