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Open data
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Basic information
Entry | Database: PDB / ID: 1kf1 | ||||||||||||||||||
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Title | Structure and Packing of Human Telomeric DNA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / QUADRUPLEX DNA / DOUBLE CHAIN REVERSAL LOOP / HUMAN TELOMERE SEQUENCE / G(ANTI).G(ANTI).G(ANTI) / PARALLEL STRANDED | Function / homology | : / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Parkinson, G.N. / Lee, M.P.H. / Neidle, S. | ![]() ![]() Title: Crystal structure of parallel quadruplexes from human telomeric DNA. Authors: Parkinson, G.N. / Lee, M.P. / Neidle, S. #1: ![]() Title: Crystal Structure of G-Quadruplex Authors: Parkinson, G.N. / Lee, M.P.H. / Neidle, S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.6 KB | Display | ![]() |
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PDB format | ![]() | 15.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.6 KB | Display | ![]() |
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Full document | ![]() | 365.6 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k8pSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % | ||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 400, potassium iodide, potassium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K | ||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 4495 / Num. obs: 4304 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 50 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 4 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 15 / Num. unique all: 440 / % possible all: 97.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 4595 / % possible obs: 98 % / Num. measured all: 50951 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 97.8 % / Rmerge(I) obs: 0.117 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K8P Resolution: 2.1→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4 / Stereochemistry target values: parkinson et al.
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rwork: 0.296 | ||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor all: 0.235 / Rfactor obs: 0.226 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.226 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.296 |