+Open data
-Basic information
Entry | Database: PDB / ID: 1n4e | ||||||
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Title | Crystal Structure of a DNA Decamer Containing a Thymine-dimer | ||||||
Components |
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Keywords | DNA / UV-damaged DNA / Thymine dimer / DNA decamer | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Park, H. / Zhang, K. / Ren, Y. / Nadji, S. / Sinha, N. / Taylor, J.-S. / Kang, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Crystal structure of a DNA decamer containing a cis-syn thymine dimer. Authors: Park, H. / Zhang, K. / Ren, Y. / Nadji, S. / Sinha, N. / Taylor, J.S. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n4e.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n4e.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n4e_validation.pdf.gz | 339.1 KB | Display | wwPDB validaton report |
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Full document | 1n4e_full_validation.pdf.gz | 379 KB | Display | |
Data in XML | 1n4e_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1n4e_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/1n4e ftp://data.pdbj.org/pub/pdb/validation_reports/n4/1n4e | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3035.003 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3053.031 Da / Num. of mol.: 2 / Source method: obtained synthetically #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 grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MgCl2, HEPES-Na, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 and 20 ℃ / pH: 8 / Details: used microseeding | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1999 / Details: mirror |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 5775 / Num. obs: 4616 / % possible obs: 88.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.3→2.39 Å / % possible all: 76.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 10325 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 76.4 % / Rmerge(I) obs: 0.198 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Cross valid method: random / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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LS refinement shell | Resolution: 2.5→2.61 Å /
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3021 |