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Open data
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Basic information
Entry | Database: PDB / ID: 3q5c | ||||||||||||||||||
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Title | Crystal structure of four-way junction with sticky end | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Sticky end | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Venkadesh, S. / Mandal, P.K. / Gautham, N. | ![]() ![]() Title: The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.6 KB | Display | ![]() |
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PDB format | ![]() | 20.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 389.4 KB | Display | ![]() |
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Full document | ![]() | 400.4 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p4yS 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: 3046.980 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized #2: 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: 45.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM DNA, 50mM Cacodylate buffer, 50mM CaCl2, 1mM spermine, 50% MPD in Reservior, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2010 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9922 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36.8 Å / Num. all: 3708 / Num. obs: 3490 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.13 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 1.4 / Num. unique all: 535 / Rsym value: 0.393 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P4Y Resolution: 2.501→29.357 Å / SU ML: 0 / Cross valid method: Throught / σ(F): 0.01 / Phase error: 41.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.602 Å2 / ksol: 0.324 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.6479 Å2
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Refinement step | Cycle: LAST / Resolution: 2.501→29.357 Å
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Refine LS restraints |
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