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- PDB-1ikk: Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ikk | ||||||||||||||||||
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Title | Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-DNA double helix / A-tract containing a T-A step | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() Mack, D.R. / Chiu, T.K. / Dickerson, R.E. | ![]() ![]() Title: Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts. Authors: Mack, D.R. / Chiu, T.K. / Dickerson, R.E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.3 KB | Display | ![]() |
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PDB format | ![]() | 15.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.1 KB | Display | ![]() |
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Full document | ![]() | 381.8 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: DNA chain | Mass: 3044.016 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: It was synthesized on a Eppendorf ECOSYN D300 Synthesizer #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: 1.84 Å3/Da / Density % sol: 33.11 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Spermine-HCL, Mg(OAc)2, MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 116 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. all: 6276 / Num. obs: 6263 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.6→1.72 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 11.2 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 65685 |
Reflection shell | *PLUS % possible obs: 98 % / Mean I/σ(I) obs: 11.17 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NDB entry bdj036 Resolution: 1.6→40 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 4 / Rfactor obs: 0.1794 / Rfactor Rwork: 0.184 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 2.32 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.72 Å / Rfactor Rfree: 0.3228 / Rfactor obs: 0.2518 |