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Yorodumi- PDB-6z18: Crystal structure of RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG; R32 form -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z18 | ||||||||||||
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Title | Crystal structure of RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG; R32 form | ||||||||||||
Components | RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG | ||||||||||||
Keywords | RNA / RNA DUPLEX 10MER / N4 / N4-dimethylcytidine | ||||||||||||
Function / homology | RNA Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||||||||
Authors | Ruszkowski, M. / Sekula, B. / Mao, S. / Haruehanroengra, P. / Sheng, J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA. Authors: Mao, S. / Sekula, B. / Ruszkowski, M. / Ranganathan, S.V. / Haruehanroengra, P. / Wu, Y. / Shen, F. / Sheng, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z18.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z18.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 6z18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/6z18 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z18 | 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: 3235.033 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 6.0, 0.012 M Spermine tetrahydrochloride, 0.012 M Sodium chloride, and 0.080 M Potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2018 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→36 Å / Num. obs: 2771 / % possible obs: 85.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 26.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.81→1.99 Å / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 231 / CC1/2: 0.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CCGGCGCCGG dimer Resolution: 1.81→35.98 Å / SU ML: 0.2079 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7659 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→35.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→35.98 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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