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Open data
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Basic information
Entry | Database: PDB / ID: 4hqh | ||||||||||||||||||||
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Title | Decamer Fluoro Carbocyclic LNA (R-F-cLNA) crystal structure | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-form DNA / carbocyclic LNA / cLNA / R-F-cLNA | Function / homology | DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() Seth, P.P. / Pallan, P.S. / Swayze, E.E. / Egli, M. | ![]() ![]() Title: Properties of a Fluorinated Carbocyclic LNA Analog Authors: Seth, P.P. / Pallan, P.S. / Swayze, E.E. / 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 | ![]() | 21.8 KB | Display | ![]() |
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PDB format | ![]() | 14.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376 KB | Display | ![]() |
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Full document | ![]() | 375.9 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ey2S 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: 3075.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 mM sodium cacodylate, pH 7.0, 40 mM potassium chloride, 6 mM Sodium Chloride, 6 mM spermine tetrahydrochloride, and 5% v/v 2-Methyl-2,4-pentanediol (MPD), 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: Feb 14, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0079 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.67 Å / Num. obs: 4674 / % possible obs: 97.3 % / Observed criterion σ(I): 5 / Redundancy: 6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.35 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.4 / Num. unique all: 244 / % possible all: 75.5 |
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Processing
Software |
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Refinement | Method to determine structure: MOL REP CCP4 Starting model: PDB ID 3EY2 Resolution: 1.8→31.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.844 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.154 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 17.861 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.804→1.851 Å / Total num. of bins used: 20
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