+Open data
-Basic information
Entry | Database: PDB / ID: 4izq | ||||||||||||||||||
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Title | GGGCATGCCC in the A-DNA Form | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | Authors | Hall, J.P. / Ruiz-Morte, S. / Murray, C.A. / Cardin, C.J. | Citation | Journal: To be Published | Title: GGGCATGCCC in the A-DNA Form Authors: Hall, J.P. / Ruiz-Morte, S. / Murray, C.A. / Cardin, C.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4izq.cif.gz | 19.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4izq.ent.gz | 12.7 KB | Display | PDB format |
PDBx/mmJSON format | 4izq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4izq_validation.pdf.gz | 375.5 KB | Display | wwPDB validaton report |
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Full document | 4izq_full_validation.pdf.gz | 375.5 KB | Display | |
Data in XML | 4izq_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 4izq_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/4izq ftp://data.pdbj.org/pub/pdb/validation_reports/iz/4izq | 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: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Purchased from ATDBio #2: 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: 2.08 Å3/Da / Density % sol: 40.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1mM 2-phenylpyridine-Pd12-cyanurate, 80mM KCl, 40mM Na-cacodylate, 20mM BaCl2, 12mM spermine, 10%(v/v) 2-methyl-2,4-pentanediol, 1ml 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, ...Details: 0.1mM 2-phenylpyridine-Pd12-cyanurate, 80mM KCl, 40mM Na-cacodylate, 20mM BaCl2, 12mM spermine, 10%(v/v) 2-methyl-2,4-pentanediol, 1ml 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.7712 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2012 |
Radiation | Monochromator: Si(111) dual crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→31.94 Å / Num. all: 3153 / Num. obs: 3153 / % possible obs: 90.7 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.04→2.09 Å / % possible all: 57.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ideal A-DNA from Coot Resolution: 2.04→31.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.963 / SU B: 6.187 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.844 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→31.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.042→2.094 Å / Total num. of bins used: 20
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