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Open data
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Basic information
Entry | Database: PDB / ID: 3uke | ||||||||||||||||||
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Title | (S)-cMOE-BNA decamer structure | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-FORM DNA / BICYCLIC NUCLEIC ACID / BNA / c-MOE-BNA / ANTISENSE OLIGONUCLEOTIDES | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() Pallan, P.S. / Egli, M. | ![]() ![]() Title: Structure and nuclease resistance of 2',4'-constrained 2'-O-methoxyethyl (cMOE) and 2'-O-ethyl (cEt) modified DNAs. Authors: Pallan, P.S. / Allerson, C.R. / Berdeja, A. / Seth, P.P. / Swayze, E.E. / Prakash, T.P. / Egli, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.3 KB | Display | ![]() |
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PDB format | ![]() | 23.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.8 KB | Display | ![]() |
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Full document | ![]() | 382.5 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ukbC ![]() 3ukcC ![]() 3ey2S C: citing same article ( 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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Unit cell |
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Components
#1: DNA chain | Mass: 3103.042 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 mM sodium cacodylate, 6 mM sodium chloride, 40 mM potassium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.007 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. all: 6270 / Num. obs: 6236 / % possible obs: 99.45 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.41 / Num. unique all: 612 / % possible all: 99.5 |
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Processing
Software |
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Refinement | Method to determine structure: MOLREP, (CCP4) Starting model: PDB entry 3EY2 Resolution: 1.68→32.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.22 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 23.174 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→32.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.72 Å / Total num. of bins used: 20
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