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Yorodumi- PDB-6fq2: Structure of minimal sequence for left -handed G-quadruplex formation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fq2 | ||||||||||||||||||||
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Title | Structure of minimal sequence for left -handed G-quadruplex formation | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | Authors | Schmitt, E. / Mechulam, Y. / Phan, A.T. / Heddi, B. / Bakalar, B. | Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2019 | Title: A Minimal Sequence for Left-Handed G-Quadruplex Formation. Authors: Bakalar, B. / Heddi, B. / Schmitt, E. / Mechulam, Y. / Phan, A.T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fq2.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fq2.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fq2_validation.pdf.gz | 346.2 KB | Display | wwPDB validaton report |
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Full document | 6fq2_full_validation.pdf.gz | 346.2 KB | Display | |
Data in XML | 6fq2_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 6fq2_validation.cif.gz | 3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/6fq2 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/6fq2 | HTTPS FTP |
-Related structure data
Related structure data | 6gz6C 4u5mS 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
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #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: 1.9 Å3/Da / Density % sol: 35.28 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 55%MPD, 12mM Spermine, 80mM KCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→26.46 Å / Num. obs: 2411 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.84 % / CC1/2: 1 / Rsym value: 0.031 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.31→2.44 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 379 / CC1/2: 0.93 / Rsym value: 0.23 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U5M Resolution: 2.31→26.46 Å / Cross valid method: FREE R-VALUE / Phase error: 27.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→26.46 Å
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Refine LS restraints |
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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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