+Open data
-Basic information
Entry | Database: PDB / ID: 3jxq | ||||||
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Title | X-Ray structure of r[CGCG(5-fluoro)CG]2 | ||||||
Components | r[CGCG(5-fluoro)CG]2 | ||||||
Keywords | RNA / double helix | ||||||
Function / homology | RNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Adamiak, D.A. / Milecki, J. / Adamiak, R.W. / Rypniewski, W. | ||||||
Citation | Journal: New J.Chem. / Year: 2010 Title: The hydration and unusual hydrogen bonding in the crystal structure of an RNA duplex containing alternating CG base pairs Authors: Adamiak, D.A. / Milecki, J. / Adamiak, R.W. / Rypniewski, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jxq.cif.gz | 25.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jxq.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/3jxq ftp://data.pdbj.org/pub/pdb/validation_reports/jx/3jxq | HTTPS FTP |
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-Related structure data
-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
#1: RNA chain | Mass: 1924.195 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: This is a modification of a naturally occuring sequence #2: Chemical | ChemComp-MG / #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: 1.89 Å3/Da / Density % sol: 34.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2.0M lithium sulfate, 10mM magnesium chloride and 50mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.1 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2001 / Details: Si(111) |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20 Å / Num. all: 9439 / Num. obs: 9439 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.041 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 409 / Rsym value: 0.296 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.655 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.307 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Total num. of bins used: 20
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