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Open data
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Basic information
Entry | Database: PDB / ID: 1y3o | ||||||||||||||||||
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Title | HIV-1 DIS RNA subtype F- Mn soaked | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / LOOP-LOOP COMPLEX / HIV-1 | Function / homology | : / RNA / RNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Ennifar, E. / Dumas, P. | ![]() ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.5 KB | Display | ![]() |
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PDB format | ![]() | 23.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394.9 KB | Display | ![]() |
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Full document | ![]() | 394.9 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xp7SC ![]() 1xpeC ![]() 1xpfC ![]() 1y3sC ![]() 1yxpC ![]() 1zciC C: citing same article ( 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
#1: RNA chain | Mass: 7465.368 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MN / #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG8000, Ammonium sulfate, MgCl2, Na Cacodylate, spermine, pH 7.0, VAPOR DIFFUSION, HANGING 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: ![]() ![]() ![]() |
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: 1.894 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 7944 / Num. obs: 7799 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 60.9 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.28 / Rsym value: 0.27 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XP7 Resolution: 2.7→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 418361.78 / 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: 32.1908 Å2 / ksol: 0.266555 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
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Xplor file |
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