+Open data
-Basic information
Entry | Database: PDB / ID: 1ih4 | ||||||||||||||||||
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Title | Multi-Conformation Crystal Structure of GGm5CGCC | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B to A DNA transition / DNA transition / structural transition | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | Authors | Vargason, J.M. / Henderson, K. / Ho, P.S. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 | Title: A crystallographic map of the transition from B-DNA to A-DNA. Authors: Vargason, J.M. / Henderson, K. / Ho, P.S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ih4.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ih4.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ih4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ih4 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ih4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1824.232 Da / Num. of mol.: 8 / Source method: obtained synthetically #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: 3.54 Å3/Da / Density % sol: 65.29 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: magnesium chloride, sodium cacodylate, spermine tetrahydrochloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2000 / Details: mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→99 Å / Num. all: 14957 / Num. obs: 14957 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 39.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.407 / % possible all: 96.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 14930 / Num. measured all: 107358 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 96.5 % / Rmerge(I) obs: 0.475 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 Stereochemistry target values: G.Parkinson, J.Vojtechovsky, L.Clowney, A.T.Brunger, H.M.Berman
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.185 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |