+Open data
-Basic information
Entry | Database: PDB / ID: 1mdg | ||||||||||||||||||
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Title | An Alternating Antiparallel Octaplex in an RNA Crystal Structure | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / tetraplex / base tetrads / base octads | Function / homology | COBALT HEXAMMINE(III) / RNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | Authors | Pan, B.C. / Xiong, Y. / Shi, K. / Sundaralingam, M. | Citation | Journal: Structure / Year: 2003 | Title: An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction Authors: Pan, B.C. / Xiong, Y. / Shi, K. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mdg.cif.gz | 13 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mdg.ent.gz | 8.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/1mdg ftp://data.pdbj.org/pub/pdb/validation_reports/md/1mdg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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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Details | The three strands of the tetraplex is generated by the four fold axis |
-Components
#1: RNA chain | Mass: 1995.093 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-NCO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.54 Å3/Da / Density % sol: 20.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: MPD, MgCl2, Cobalt(III)hexammine, ethidine bromide, sodium cacodylate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9195, 0.9192, 0.800 | ||||||||||||
Detector | Type: ENRAF-NONIUS / Detector: CCD / Date: May 31, 2001 / Details: mirrors | ||||||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→30 Å / Num. all: 3807 / Num. obs: 3800 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 41.7 % / Rsym value: 0.056 | ||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Num. unique all: 364 / Rsym value: 0.309 / % possible all: 98.6 | ||||||||||||
Reflection | *PLUS Num. measured all: 158438 / Rmerge(I) obs: 0.056 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→30 Å / Isotropic thermal model: isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refinement | *PLUS Highest resolution: 1.5 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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