+
Open data
-
Basic information
Entry | Database: PDB / ID: 1qph | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE A-DNA DODECAMER GACCACGTGGTC | ||||||||||||||||||
![]() | 5'-D(P*![]() DNA / DOUBLE HELIX / A-DNA / MAX PROTEIN / DNA CURVATURE | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() Raaijmakers, H. / Suck, D. / Mayer, C. | ![]() ![]() Title: Crystal Structure Analysis of the A-DNA Dodecamer GACCACGTGGTC Authors: Raaijmakers, H. / Suck, D. / Mayer, C. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 16.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 10.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 318 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 318 KB | Display | |
Data in XML | ![]() | 1.2 KB | Display | |
Data in CIF | ![]() | 1.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RECOGNITION SEQUENCE OF MAX PROTEIN |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.88 % | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: (NH4)2SO4, WATER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 278 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→23 Å / Num. all: 1781 / Num. obs: 1781 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 43.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: NDB ID ADL045 Resolution: 2.5→7 Å / σ(F): 2 Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING STRUCTURES, ACTA CRYST. D, 52, 57-64 (1996). Details: SIMULATED ANNEALING REFINEMENT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARAM_NDBX3.DNA / Topol file: TOP_NDBX3.DNA |