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- PDB-344d: DETERMINATION BY MAD-DM OF THE STRUCTURE OF THE DNA DUPLEX D(ACGT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 344d | ||||||||||||||||||
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Title | DETERMINATION BY MAD-DM OF THE STRUCTURE OF THE DNA DUPLEX D(ACGTACG(5-BRU))2 AT 1.46A AND 100K | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / A-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Todd, A.R. / Adams, A. / Powell, H.R. / Cardin, C.J. | ![]() ![]() Title: Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 A and 100 K. Authors: Todd, A.K. / Adams, A. / Powell, H.R. / Wilcock, D.J. / Thorpe, J.H. / Lausi, A. / Zanini, F. / Wakelin, L.P. / Cardin, C.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 21.4 KB | Display | ![]() |
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PDB format | ![]() | 15 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 316.5 KB | Display | ![]() |
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Full document | ![]() | 326.3 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 243dS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 2491.487 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 285 K / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1996 / Details: MIRROR |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.4→15 Å / Num. obs: 8062 / % possible obs: 98.3 % / Redundancy: 4.35 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 0.137 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.137 / % possible all: 60.1 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 15 Å / % possible obs: 98.3 % / Redundancy: 4.35 % |
Reflection shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.45 Å / % possible obs: 60.1 % / Redundancy: 1.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NDB ENTRY ADH070 (PDB ENTRY 243D) Highest resolution: 1.46 Å / Num. parameters: 2232 / Num. restraintsaints: 2730 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
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Solvent computation | Solvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 245 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.46 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 4312 / σ(F): 0 / Rfactor all: 0.1115 / Rfactor obs: 0.109 / Rfactor Rfree: 0.2003 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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