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Yorodumi- PDB-1i1p: REFINEMENT INCLUDING EXPERIMENTAL MAD PHASES ALLOWS AN EXHAUSTIVE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i1p | ||||||
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Title | REFINEMENT INCLUDING EXPERIMENTAL MAD PHASES ALLOWS AN EXHAUSTIVE STUDY OF ORDERED SOLVENT MOLECULES FOR A PLATINATED DECANUCLEOTIDE | ||||||
Components |
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Keywords | DNA / ANTITUMOR DRUG / CIS-DDP / INTERSTRAND CROSS-LINK / DEOXYRIBONUCLEIC ACID / SPERMINE | ||||||
Function / homology | Cisplatin / SPERMINE / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å | ||||||
Authors | Coste, F. / Shepard, W. / Zelwer, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Description of ordered solvent molecules in a platinated decanucleotide duplex refined at 1.6A resolution against experimental MAD phases. Authors: Coste, F. / Shepard, W. / Zelwer, C. #1: Journal: Nucleic Acids Res. / Year: 1999 Title: Crystal Structure of a Double-Stranded DNA Containing A Cisplatin Interstrand Cross-Link At 1.63 Angstrom Resolution: Hydration At The Platinated Site Authors: Coste, F. / Malinge, J.M. / Serre, L. / Shepard, W. / Roth, M. / Leng, M. / Zelwer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i1p.cif.gz | 24.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i1p.ent.gz | 15.6 KB | Display | PDB format |
PDBx/mmJSON format | 1i1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i1p_validation.pdf.gz | 385.7 KB | Display | wwPDB validaton report |
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Full document | 1i1p_full_validation.pdf.gz | 387.8 KB | Display | |
Data in XML | 1i1p_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1i1p_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1p ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1p | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2931.917 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3159.079 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-CPT / |
#4: Chemical | ChemComp-SPM / |
#5: 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: 2.34 Å3/Da / Density % sol: 47.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: sodium cacodylate, NaCl, KCl, spermine, MPD, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1.0906,1.0718,1.0711,1.0301 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 | |||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.63→20 Å / Num. all: 7353 / Num. obs: 7333 / % possible obs: 93.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14 | |||||||||||||||
Reflection shell | Resolution: 1.63→1.72 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / % possible all: 97 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.037 | |||||||||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.63→20 Å / Stereochemistry target values: Hendrikson & Konnert
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Refinement step | Cycle: LAST / Resolution: 1.63→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.1883 / Rfactor Rwork: 0.1585 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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