+Open data
-Basic information
Entry | Database: PDB / ID: 1d9r | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / TANDEM GA BASE PAIRS / GA MISMATCH / DEOXYRIBONUCLEIC ACID | Function / homology | COBALT HEXAMMINE(III) / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING BY BROMINES / Resolution: 1.5 Å | Authors | Gao, Y.-G. / Robinson, H. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J. | Citation | Journal: Biochemistry / Year: 1999 | Title: Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution. Authors: Gao, Y.G. / Robinson, H. / Sanishvili, R. / Joachimiak, A. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d9r.cif.gz | 25.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d9r.ent.gz | 16 KB | Display | PDB format |
PDBx/mmJSON format | 1d9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d9r_validation.pdf.gz | 389.5 KB | Display | wwPDB validaton report |
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Full document | 1d9r_full_validation.pdf.gz | 392 KB | Display | |
Data in XML | 1d9r_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 1d9r_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d9r ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d9r | HTTPS FTP |
-Related structure data
Related structure data | 1d8xC 1dcrC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3158.913 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NCO / | #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 | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MPD, COBALT HEXAMMINE, MGCL2, TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9611 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 16, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9611 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→10 Å / Num. all: 8923 / Num. obs: 8923 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.5→1.56 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.377 / % possible all: 100 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MAD PHASING BY BROMINES / Resolution: 1.5→10 Å / Num. parameters: 2220 / Num. restraintsaints: 1837 / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 Stereochemistry target values: G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, H.M.BERMAN Details: SHELXL HOPE OPTION
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Solvent computation | Solvent model: SHELXL SWAT OPTION | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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