+Open data
-Basic information
Entry | Database: PDB / ID: 2plo | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | D-(GTATACC) low temperature (100K) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / HIGH PRESSURE / LOW TEMPERATURE / COMPRESSIBILITY / CRYSTALS | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | Authors | Prange, T. / Lecouvey, M. / Migianu-Griffoni, E. | Citation | Journal: To be Published Title: Adaptation of macromolecular crystals to extreme conditions: high pressure versus low temperature Authors: Prange, T. / Girard, E. / Kahn, R. / Lecouvey, M. / Migianu-Griffoni, E. / Mezouar, M. / Fourme, R. #1: Journal: To be Published Title: Adaptation of base paired double helix architecture to extreme pressure Authors: Girard, E. / Prange, T. / Dhaussy, A.C. / Migianu-Griffoni, E. / Lecouvey, M. / Chervin, J.C. / Mezouar, M. / Kahn, R. / Fourme, R. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2plo.cif.gz | 19.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2plo.ent.gz | 12.2 KB | Display | PDB format |
PDBx/mmJSON format | 2plo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/2plo ftp://data.pdbj.org/pub/pdb/validation_reports/pl/2plo | HTTPS FTP |
---|
-Related structure data
Related structure data | 2pl8S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | A form of DNA - double stranded helix |
-Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: automated solid synthesis #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.21 % | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20 mg dissolved in 0.2 ml of 15 % MPD, 10-2 M sodium cacodylate buffer. Additives : 10-5M sodium azide, 10-2 M MgCl2 and 2.10-2 M spermine chloride, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.962 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2006 / Details: Si(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.962 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→10 Å / Num. obs: 9382 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2PL8 Resolution: 1.4→10 Å / Num. parameters: 1579 / Num. restraintsaints: 1606 / Isotropic thermal model: individual isotropic B factors / Cross valid method: NONE / σ(F): 2 / σ(I): 4
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 182 / Occupancy sum non hydrogen: 393 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|