+Open data
-Basic information
Entry | Database: PDB / ID: 7f8z | ||||||||||||||||||||
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Title | RNA kink-turn motif with 2-aminopurine | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / 2-aminopurine / kink-turn motif | Function / homology | : / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | Authors | Kondo, J. / Miyauchi, T. | Citation | Journal: To Be Published | Title: RNA kink-turn motif with 2-aminopurine Authors: Kondo, J. / Miyauchi, T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f8z.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f8z.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 7f8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f8z_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 7f8z_full_validation.pdf.gz | 455.3 KB | Display | |
Data in XML | 7f8z_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 7f8z_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/7f8z ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f8z | HTTPS FTP |
-Related structure data
Related structure data | 7ei7C 7ei8C 4c40S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: RNA chain | Mass: 6217.834 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: 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: 2.89 Å3/Da / Density % sol: 57.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: MPD, spermine tetrahydrochloride, potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 19, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→35.04 Å / Num. obs: 14856 / % possible obs: 98.7 % / Redundancy: 5.796 % / Biso Wilson estimate: 44.299 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.109 / Χ2: 0.922 / Net I/σ(I): 14.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C40 Resolution: 3→35.04 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.65 / Stereochemistry target values: ML
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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 max: 99.3 Å2 / Biso mean: 35.2233 Å2 / Biso min: 15.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→35.04 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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