+Open data
-Basic information
Entry | Database: PDB / ID: 6xus | ||||||
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Title | RNA dodecamer with a 6-hydrazino-2-aminopurine modified base | ||||||
Components | RNA dodecamer with a 6-hydrazino-2-aminopurine modified base | ||||||
Keywords | RNA / 6-hydrazino-2-aminopurine modified base | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Ennifar, E. / Micura, R. / Gasser, C. / Brillet, K. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL). Authors: Gasser, C. / Delazer, I. / Neuner, E. / Pascher, K. / Brillet, K. / Klotz, S. / Trixl, L. / Himmelstoss, M. / Ennifar, E. / Rieder, D. / Lusser, A. / Micura, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xus.cif.gz | 38.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xus.ent.gz | 23.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xus_validation.pdf.gz | 273.9 KB | Display | wwPDB validaton report |
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Full document | 6xus_full_validation.pdf.gz | 273.9 KB | Display | |
Data in XML | 6xus_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 6xus_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/6xus ftp://data.pdbj.org/pub/pdb/validation_reports/xu/6xus | HTTPS FTP |
-Related structure data
Related structure data | 6xurC 2q1rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 3881.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: MPD, Na Cacodylate, spermine, NaCl, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 106381 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.68 Å2 / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 13.32 |
Reflection shell | Resolution: 1.04→1.07 Å / Mean I/σ(I) obs: 0.29 / Num. unique obs: 1200 / CC1/2: 0.148 / Rrim(I) all: 261 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q1R Resolution: 1.1→24.62 Å / SU ML: 0.1782 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5847 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.5 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→24.62 Å
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Refine LS restraints |
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LS refinement shell |
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