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- PDB-1wqy: X-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wqy | ||||||||||||||||||
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Title | X-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal grown in D2O solution | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-DNA / HYDRATION / HYDROGEN | Function / homology | DEUTERATED WATER / DNA | ![]() Method | ![]() ![]() ![]() ![]() Arai, S. / Chatake, T. / Ohhara, T. / Kurihara, K. / Tanaka, I. / Suzuki, N. / Fujimoto, Z. / Mizuno, H. / Niimura, N. | ![]() ![]() Title: Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements Authors: Arai, S. / Chatake, T. / Ohhara, T. / Kurihara, K. / Tanaka, I. / Suzuki, N. / Fujimoto, Z. / Mizuno, H. / Niimura, 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 | ![]() | 21.4 KB | Display | ![]() |
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PDB format | ![]() | 13.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.6 KB | Display | ![]() |
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Full document | ![]() | 364.5 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wqzC ![]() 167dS S: Starting model for refinement C: citing same article ( |
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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: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-DOD / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.12 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: batch (d2o) / pH: 7 Details: 30% MPD, 0.1M MAGNESIUM CHLORIDE, 0.1M SODIUM CACODYLATE, 0.002M DNA, pD 6.6, pH 7.0, BATCH (D2O), temperature 279K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: IMAGE PLATE / Date: Jun 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 8528 / Num. obs: 8451 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 9.27 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.025 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.25 % / Rmerge(I) obs: 0.108 / Num. unique all: 828 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 167D Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: LIMITING RESOLUTION ESTIMATED FROM DATA COLLECTION STATISTICS WAS 1.6 ANGSTROMS. HOWEVER, THE STRUCTURAL REFINEMENT PROCESSING WAS COMPUTED BY USING REFLECTIONS 2.0 - 50.0 ANGSTROMS BECAUSE ...Details: LIMITING RESOLUTION ESTIMATED FROM DATA COLLECTION STATISTICS WAS 1.6 ANGSTROMS. HOWEVER, THE STRUCTURAL REFINEMENT PROCESSING WAS COMPUTED BY USING REFLECTIONS 2.0 - 50.0 ANGSTROMS BECAUSE THE BIN R VALUE AND BIN FREE R VALUE OF RESOLUTION RANGE HIGHER THAN 2.0 ANGSTROMS WERE VERY HIGH.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.048
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