+Open data
-Basic information
Entry | Database: PDB / ID: 2i5a | ||||||||||||||||||
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Title | Crystal structure of a DB1055-D(CGCGAATTCGCG)2 complex | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-type DNA dodecamer with compound DB 1055 | Function / homology | Chem-M1B / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | Authors | Neidle, S. / Lee, M.P.H. | Citation | Journal: To be Published | Title: Crystal structure of a DB1055-D(CGCGAATTCGCG)2 complex Authors: Neidle, S. / Lee, M.P.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i5a.cif.gz | 26.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i5a.ent.gz | 16.2 KB | Display | PDB format |
PDBx/mmJSON format | 2i5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i5a_validation.pdf.gz | 614.1 KB | Display | wwPDB validaton report |
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Full document | 2i5a_full_validation.pdf.gz | 612 KB | Display | |
Data in XML | 2i5a_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 2i5a_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/2i5a ftp://data.pdbj.org/pub/pdb/validation_reports/i5/2i5a | HTTPS FTP |
-Related structure data
Related structure data | 2dbeS S: Starting model for refinement |
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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: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-M1B / | #4: 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: 2.07 Å3/Da / Density % sol: 40.56 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: MAGNESIUM CHLORIDE, DNA DODECAMER, MPD, COMPOUND DB 1055, SODIUM CACODYLATE BUFFER, pH 7, VAPOR DIFFUSION, HANGING DROP, pH 7.00 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 17, 2006 / Details: OSMIC FOCUSING MIRROR SYSTEM |
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: 1.65→25 Å / Num. obs: 7580 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.91 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 33.42 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.8 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DBE Resolution: 1.65→8 Å / Num. parameters: 2359 / Num. restraintsaints: 2359 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 598 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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