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Open data
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Basic information
Entry | Database: PDB / ID: 1mf5 | ||||||||||||||||||
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Title | GCATGCT Quadruplex | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / QUADRUPLEX / ATOMIC RESOLUTION | Function / homology | COBALT HEXAMMINE(III) / DNA | ![]() Method | ![]() ![]() ![]() ![]() Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Cardin, C.J. | ![]() ![]() Title: Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution Authors: Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Cardin, C.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.9 KB | Display | ![]() |
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PDB format | ![]() | 17.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 401.2 KB | Display | ![]() |
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Full document | ![]() | 405.4 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 2113.410 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NCO / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: Cobalt Hexammine, Cacodylate, MPD, NaCl, KCl, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 290 K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→29.62 Å / Num. obs: 12514 / % possible obs: 99.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 18.213 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.96 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 6.59 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.24 / Num. unique all: 2803 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Num. obs: 2803 / Redundancy: 7.7 % / Num. measured all: 12514 |
Reflection shell | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 1.2 Å / % possible obs: 99.4 % / Redundancy: 6.64 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: UDG028 Resolution: 1.1→20 Å / Num. parameters: 2924 / Num. restraintsaints: 2847 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 175 / Occupancy sum non hydrogen: 322 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.224 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 1.2 Å / Rfactor Rfree: 0.2173 / Rfactor Rwork: 0.208 |