+Open data
-Basic information
Entry | Database: PDB / ID: 1y3s | ||||||||||||||||||
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Title | HIV-1 DIS RNA subtype F- MPD form | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / LOOP-LOOP COMPLEX / HIV-1 | Function / homology | : / RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | Authors | Ennifar, E. / Dumas, P. | Citation | Journal: J.Mol.Biol. / Year: 2006 | Title: Polymorphism of Bulged-out Residues in HIV-1 RNA DIS Kissing Complex and Structure Comparison with Solution Studies. Authors: Ennifar, E. / Dumas, P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y3s.cif.gz | 39 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y3s.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 1y3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/1y3s ftp://data.pdbj.org/pub/pdb/validation_reports/y3/1y3s | HTTPS FTP |
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-Related structure data
Related structure data | 1xp7C 1xpeC 1xpfC 1y3oC 1yxpC 1zciC C: citing same article (ref.) |
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Similar structure data |
-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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-Components
#1: RNA chain | Mass: 7465.368 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Chemical | #4: 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: 2.54 Å3/Da / Density % sol: 51.6 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, spermine, KCl, MgCl2, Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 310K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9196 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 5, 2004 |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. all: 13794 / Num. obs: 13511 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 61.9 Å2 / Rsym value: 0.056 / Net I/σ(I): 30.86 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 4.35 / Rsym value: 0.383 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 618415.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.0914 Å2 / ksol: 0.344799 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.35 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
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Xplor file |
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