+Open data
-Basic information
Entry | Database: PDB / ID: 7rqt | ||||||||||||||||||||||||||||
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Title | THE B-DNA DODECAMER With HIGH RESOLUTION | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / Dodecamer | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 Å | Authors | Chen, C. / Huang, Z. | Funding support | United States, 1items |
Citation | Journal: Cryst.Growth Des. / Year: 2022 | Title: 2'-beta-Selenium Atom on Thymidine to Control beta-Form DNA Conformation and Large Crystal Formation Authors: Chen, C. / Fang, Z. / Huang, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rqt.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rqt.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rqt_validation.pdf.gz | 378.5 KB | Display | wwPDB validaton report |
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Full document | 7rqt_full_validation.pdf.gz | 378.5 KB | Display | |
Data in XML | 7rqt_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 7rqt_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/7rqt ftp://data.pdbj.org/pub/pdb/validation_reports/rq/7rqt | HTTPS FTP |
-Related structure data
Related structure data | 355dS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / | #3: 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: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2-Methyl-2,4-pentanedial, sodium cacodylate trihydrate, spermine tetrahydrochloride, sodium chloride, potassium chloride, magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.969 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.26→50 Å / Num. obs: 18494 / % possible obs: 98 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.06 / Χ2: 0.908 / Net I/σ(I): 18.7 / Num. measured all: 253507 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 355D Resolution: 1.26→34.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.736 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.49 Å2 / Biso mean: 16.404 Å2 / Biso min: 10.1 Å2
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Refinement step | Cycle: final / Resolution: 1.26→34.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.262→1.295 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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