+Open data
-Basic information
Entry | Database: PDB / ID: 1l3z | ||||||||||||||||||
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Title | Crystal Structure Analysis of an RNA Heptamer | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA | Function / homology | RNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.01 Å | Authors | Shi, K. / Pan, B. / Sundaralingam, M. | Citation | Journal: Nucleic Acids Res. / Year: 2003 | Title: The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs Authors: Shi, K. / Pan, B. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l3z.cif.gz | 17 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l3z.ent.gz | 10.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/1l3z ftp://data.pdbj.org/pub/pdb/validation_reports/l3/1l3z | 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 2205.379 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: MPD, CaCl2, Cacodylate buffer, pH7.0 | ||||||||||||||||||||||||||||||||||||||||||
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: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→50 Å / Num. obs: 22206 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.1 Å2 |
Reflection shell | Resolution: 2.01→2.13 Å |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 2840 / Rmerge(I) obs: 0.054 |
-Processing
Software |
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Refinement | Resolution: 2.01→20 Å / Rfactor Rfree error: 0.014 / Data cutoff high rms absF: 545644.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 30.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.13 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Refinement | *PLUS Rfactor Rfree: 0.185 / Rfactor Rwork: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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