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Open data
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Basic information
Entry | Database: PDB / ID: 3v07 | ||||||||||||||||||
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Title | Crystal structure of R-6'-Me-3'-fluoro hexitol nucleic acid | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-form DNA / 3'-fluoro hexitol nucleic acid / FHNA / R-6'-Me-FHNA / antisense oligonucleotides | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Pallan, P.S. / Egli, M. | ![]() ![]() Title: Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid. Authors: Pallan, P.S. / Yu, J. / Allerson, C.R. / Swayze, E.E. / Seth, 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 | ![]() | 35.4 KB | Display | ![]() |
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PDB format | ![]() | 25 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383 KB | Display | ![]() |
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Full document | ![]() | 390.8 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v06C ![]() 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: 3091.049 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: 2.19 Å3/Da / Density % sol: 43.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 40 mM sodium cacodylate, 80 mM sodium chloride, 12 mM spermine tetrahydrochloride, 10% 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2010 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→31.45 Å / Num. all: 15944 / Num. obs: 15617 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 47 |
Reflection shell | Resolution: 1.24→1.27 Å / % possible all: 88.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EY2 Resolution: 1.24→31.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.361 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.044 / ESU R Free: 0.048 / 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: 18.337 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→31.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.24→1.273 Å / Total num. of bins used: 20
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