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- PDB-6x5d: Structure of Dickerson-Drew Dodecamer with 2'-MeSe-ara-T modification -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x5d | ||||||||||||||||||||||||||||
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Title | Structure of Dickerson-Drew Dodecamer with 2'-MeSe-ara-T modification | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Selenium modification | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() ![]() Chen, C. / Fang, Z. / Huang, Z. | Funding support | | ![]()
![]() ![]() Title: 2'-Beta-Selenium Atom on Thymidine to Control Beta-Form DNA Conformation and Large Crystal Formation Authors: Chen, C. / Fang, Z. / Huang, Z. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 28.6 KB | Display | ![]() |
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PDB format | ![]() | 17.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.8 KB | Display | ![]() |
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Full document | ![]() | 379.9 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 355dS 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: 3756.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2-Methyl-2,4-pentanediol, Sodium cacodylate trihydrate, Spermine tetrahydrochloride, Sodium chloride, Potassium chloride, Magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2019 |
Radiation | Monochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. obs: 24146 / % possible obs: 98.6 % / Redundancy: 13.5 % / Biso Wilson estimate: 17.9 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.011 / Rrim(I) all: 0.04 / Χ2: 0.916 / Net I/σ(I): 45 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.249 / Num. unique obs: 1078 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.077 / Rrim(I) all: 0.262 / Χ2: 0.92 / % possible all: 93.5 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 355D Resolution: 1.15→34.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 0.555 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 49.21 Å2 / Biso mean: 17.935 Å2 / Biso min: 11.79 Å2
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Refinement step | Cycle: final / Resolution: 1.15→34.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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