+Open data
-Basic information
Entry | Database: PDB / ID: 8clm | ||||||
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Title | 1.80 A crystal structure of RNA/2'-O-methyl-RNA heteroduplex | ||||||
Components |
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Keywords | RNA / RNA/2'-OMeRNA heteroduplex | ||||||
Function / homology | : / RNA Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dolot, R.M. / Maciaszek, A. / Nawrot, B.C. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of RNA/2'-O-methyl-RNA heteroduplex Authors: Dolot, R.M. / Maciaszek, A. / Mikolajczyk, B. / Nawrot, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8clm.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8clm.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 8clm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8clm_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 8clm_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 8clm_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 8clm_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/8clm ftp://data.pdbj.org/pub/pdb/validation_reports/cl/8clm | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 2808.703 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: RNA chain | Mass: 2941.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.28 Å3/Da / Density % sol: 46.06 % / Description: prism |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1 mM duplex, 1.4 M Li2SO4, 50 mM sodium cacodylate, 1 mM spermine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.011 Å / Num. obs: 15124 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.046 / Rrim(I) all: 0.094 / Χ2: 0.99 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 868 / CC1/2: 0.817 / Rpim(I) all: 0.382 / Rrim(I) all: 0.747 / Χ2: 1.01 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.011 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.644 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.151 Details: Hydrogens have been added in their riding positions
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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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.582 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.011 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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