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- PDB-4f3u: Crystal structure of 5-hydroxy-2'-deoxycytidine base paired with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f3u | ||||||||||||||||||||
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Title | Crystal structure of 5-hydroxy-2'-deoxycytidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / 5-hydroxy-dC / modified Dickerson / 5-hydroxy-2'-deoxycytidine | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic (others) | Method | ![]() ![]() ![]() ![]() Szulik, M.W. / Nocek, B. / Joachimiak, A. / Stone, M.P. | ![]() ![]() Title: Crystal structure of 5-hydroxy-2'-deoxycytidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer Authors: Szulik, M.W. / Nocek, B. / Joachimiak, A. / Stone, M.P. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.8 KB | Display | ![]() |
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PDB format | ![]() | 28.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.2 KB | Display | ![]() |
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Full document | ![]() | 381.6 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 436dS 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: 3679.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic (others) #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MPD, 40mM sodium cacodylate, 12 mM spermine-tetra-HCl, 80mM sodium chloride, 20mM magnesium chloride., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2012 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→25 Å / Num. all: 13718 / Num. obs: 13485 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 1.4→1.42 Å / % possible all: 95.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 436D Resolution: 1.401→25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.612 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.401→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.438 Å / Total num. of bins used: 20
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