+Open data
-Basic information
Entry | Database: PDB / ID: 1ih6 | ||||||||||||||||||
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Title | Multi-Conformation Crystal Structure of GGBr5CGCC | ||||||||||||||||||
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 / SYNCHROTRON / MAD / Resolution: 1.45 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 | 1ih6.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ih6.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ih6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ih6_validation.pdf.gz | 391.8 KB | Display | wwPDB validaton report |
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Full document | 1ih6_full_validation.pdf.gz | 401.5 KB | Display | |
Data in XML | 1ih6_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1ih6_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ih6 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ih6 | HTTPS FTP |
-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: 1889.101 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: 2.81 Å3/Da / Density % sol: 56.22 % | ||||||||||||||||||||||||||||||||||||
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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: 105 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92042, 0.92065, 0.90836 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2000 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.45→20 Å / Num. all: 58509 / Num. obs: 58509 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 22 | ||||||||||||
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 9 % / Rmerge(I) obs: 0.589 / % possible all: 99.6 | ||||||||||||
Reflection | *PLUS Num. measured all: 628716 / Rmerge(I) obs: 0.11 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.668 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.45→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Chad C. Sines for SHELXL Details: This structure was solved using data collected at the peak of Bromine absorption. As a result, the structure factors of the unique reflections and bijvoets have been kept separate for ...Details: This structure was solved using data collected at the peak of Bromine absorption. As a result, the structure factors of the unique reflections and bijvoets have been kept separate for deposition. In addition, the correct calculation for R-factor should take into the account the appropriate scattering factors (f' & f'') at this wavelength.
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Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.138 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |