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Yorodumi- PDB-3gcy: Crystal studies of d(CACGCG).d(CGCGTG) grown in presence of calci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gcy | ||||||
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Title | Crystal studies of d(CACGCG).d(CGCGTG) grown in presence of calcium chloride | ||||||
Components |
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Keywords | DNA / Z-form DNA duplex with Watson-Crick base pairing | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mandal, P.K. / Venkadesh, S. / Nandini, M. / Gautham, N. | ||||||
Citation | Journal: To be Published Title: Crystal studies of d(CACGCG).d(CGCGTG) grown with various metal ions Authors: Mandal, P.K. / Venkadesh, S. / Nandini, M. / Gautham, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gcy.cif.gz | 16 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gcy.ent.gz | 10 KB | Display | PDB format |
PDBx/mmJSON format | 3gcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gcy_validation.pdf.gz | 376.1 KB | Display | wwPDB validaton report |
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Full document | 3gcy_full_validation.pdf.gz | 377.2 KB | Display | |
Data in XML | 3gcy_validation.xml.gz | 3 KB | Display | |
Data in CIF | 3gcy_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/3gcy ftp://data.pdbj.org/pub/pdb/validation_reports/gc/3gcy | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: 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: 1.64 Å3/Da | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.99 Details: Sodium Cacodylate 50mM, Calcium chloride 140mM, Spermine 1mM, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2009 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 2431 / Num. obs: 2334 / % possible obs: 95.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.37 Å2 / Rmerge(I) obs: 0.1026 / Rsym value: 0.0888 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.27 % / Rmerge(I) obs: 0.3416 / Mean I/σ(I) obs: 1.3 / Num. unique all: 226 / Rsym value: 0.2905 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Z-DNA FIBER MODEL BUILT WITH INSIGHT-II Resolution: 1.8→15.12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.213 / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.708 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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