+Open data
-Basic information
Entry | Database: PDB / ID: 5xk0 | ||||||||||||||||||||||||||||
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Title | Structure of 8-mer DNA2 | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / duplex | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.451 Å | Authors | Liu, H.H. / Gan, J.H. | Funding support | China, 1items |
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 | Title: A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs Authors: Liu, H.H. / Shen, F.S. / Haruehanroengra, P. / Yao, Q.Q. / Cheng, Y.S. / Chen, Y.Q. / Yang, C. / Zhang, J. / Wu, B.X. / Luo, Q. / Cui, R.X. / Li, J.X. / Ma, J.B. / Sheng, J. / Gan, J.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xk0.cif.gz | 20 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xk0.ent.gz | 11.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xk0_validation.pdf.gz | 345.9 KB | Display | wwPDB validaton report |
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Full document | 5xk0_full_validation.pdf.gz | 345.9 KB | Display | |
Data in XML | 5xk0_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 5xk0_validation.cif.gz | 3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/5xk0 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/5xk0 | HTTPS FTP |
-Related structure data
Related structure data | 5xjzC 5xk1C 5wspS 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: 2412.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
-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: 46.23 % / Description: diamond |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% v/v MPD, 40mM Sodium cacodylate pH 6.0, 12mM Spermine tetra-HCl, 80mM KCl, 20mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. obs: 4199 / % possible obs: 98.6 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 82.3 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 358 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5WSP Resolution: 1.451→29.707 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.451→29.707 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4513→1.5 Å
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Refinement TLS params. | Method: refined / Origin x: 9.5067 Å / Origin y: 9.0897 Å / Origin z: 2.4899 Å
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Refinement TLS group | Selection details: all |