+Open data
-Basic information
Entry | Database: PDB / ID: 3czw | ||||||||||||||||||
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Title | X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / duplex / base pairing / G(syn) - G(anti) / sulphate anion | Function / homology | RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | Authors | Rypniewski, W. / Adamiak, D.A. / Milecki, J. / Adamiak, R.W. | Citation | Journal: Rna / Year: 2008 | Title: Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex. Authors: Rypniewski, W. / Adamiak, D.A. / Milecki, J. / Adamiak, R.W. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3czw.cif.gz | 20.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3czw.ent.gz | 12.5 KB | Display | PDB format |
PDBx/mmJSON format | 3czw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/3czw ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3czw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 5170.103 Da / Num. of mol.: 1 Fragment: duplex formed by the shorter strands of hammerhead ribozyme Source method: obtained synthetically |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.46 Å3/Da / Density % sol: 49.95 % | ||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.3 M lithium sulphate, 100 mM cacodylate buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8115 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 26, 2004 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8115 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 9874 / Num. obs: 9874 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.082 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.76 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: a short duplex GUCU:CGGA taken from NDB: RR0033 Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.392 / SU ML: 0.076 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.065 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.537 Å2
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Refine analyze | Luzzati coordinate error free: 0.06 Å / Luzzati sigma a free: 0.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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