+
Open data
-
Basic information
Entry | Database: PDB / ID: 1cw9 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / CROSSLINKED DOUBLE-HELICAL DNA / BASE-PAIR OPENING / PARTIAL BASE FLIPPING. | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() van Aalten, D.M.F. / Erlanson, D.A. / Verdine, G.L. / Joshua-Tor, L. | ![]() ![]() Title: A structural snapshot of base-pair opening in DNA. Authors: van Aalten, D.M. / Erlanson, D.A. / Verdine, G.L. / Joshua-Tor, L. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 38.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 341.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 341.7 KB | Display | |
Data in XML | ![]() | 2.1 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 3106.110 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: CROSSLINKED DNA WAS SYNTHESIZED BY THE CONVERTIBLE NUCLEOSIDE APPROACH #2: Chemical | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, CALCIUM CHLORIDE, SODIUM CHLORIDE, SPERMINE TETRACHLORIDE, SODIUM CACODYLATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→13 Å / Num. all: 62990 / Num. obs: 62990 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 98 |
Reflection | *PLUS Num. obs: 15570 / Num. measured all: 62990 |
Reflection shell | *PLUS % possible obs: 98 % / Num. unique obs: 1555 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: BDJ017 Resolution: 1.55→13 Å / Isotropic thermal model: RESTRAINED CNS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: CNS NUCLEIC ACID PARAMETERS USING SOFT VAN DER WAALS PARAMETERS (PARKINSON ET AL., ACTA D, 52, 57-64 (1996)). Details: MAXIMUM LIKELIHOOD.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT - CNS CALCULATED MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.61 Å / % reflection Rfree: 5 % / % reflection obs: 98 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: DNA-RNA_REP.PARAM / Topol file: DNA-RNA.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 13 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 5 % |