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Yorodumi- PDB-4agz: CRYSTAL STRUCTURE OF THE DB 985-D(CGCGAATTCGCG)2 COMPLEX AT 1.25 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4agz | ||||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF THE DB 985-D(CGCGAATTCGCG)2 COMPLEX AT 1.25 A RESOLUTION. | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA DOUBLE HELIX / DNA-DRUG COMPLEX / DNA HYDRATION | Function / homology | Chem-D98 / DNA / DNA (> 10) | Function and homology information Biological species | SYNTHETIC CONSTRUCT (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | Authors | Munnur, D.G. / Mitchell, E.P. / Forsyth, V.T. / Teixeira, S.C.M. / Neidle, S. | Citation | Journal: To be Published | Title: A Detailed Study of Water Network in the Minor Groove of D(Cgcgaattcgcg)2 and D(Cgcaaatttgcg)2 in Presence of Linear Groove Binders Authors: Munnur, D.G. / Mitchell, E.P. / Forsyth, V.T. / Teixeira, S.C.M. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4agz.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4agz.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 4agz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4agz_validation.pdf.gz | 621.1 KB | Display | wwPDB validaton report |
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Full document | 4agz_full_validation.pdf.gz | 627.5 KB | Display | |
Data in XML | 4agz_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 4agz_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/4agz ftp://data.pdbj.org/pub/pdb/validation_reports/ag/4agz | HTTPS FTP |
-Related structure data
Related structure data | 4ah0C 4ah1C 1fq2S C: citing same article (ref.) 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 / Source: (synth.) SYNTHETIC CONSTRUCT (others) #2: Chemical | #3: Chemical | ChemComp-D98 / | #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: 2.16 Å3/Da / Density % sol: 61.58 % / Description: NONE |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MAGNESIUM CHLORIDE, DNA, DB 985, MPD, SODIUM CACODYLATE BUFFER. PH 6.6, VAPOUR DIFFUSION, SITTING DROP, 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 19, 2009 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→39.9 Å / Num. obs: 18006 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FQ2 Resolution: 1.25→14.76 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.359 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→14.76 Å
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