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Open data
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Basic information
Entry | Database: PDB / ID: 2gpx | ||||||||||||||||||
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Title | 2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / 2'-Methylseleno-uridine / Se-DNA / Se-Br-DNA / Selenium Derivatization | Function / homology | : / DNA | ![]() Method | ![]() ![]() ![]() Jiang, J. / Huang, Z. | ![]() ![]() Title: Selenium derivatization of nucleic acids for crystallography. Authors: Jiang, J. / Sheng, J. / Carrasco, N. / Huang, Z. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.7 KB | Display | ![]() |
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PDB format | ![]() | 8.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.6 KB | Display | ![]() |
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Full document | ![]() | 372.6 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 3.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1z7iSC ![]() 2dljC ![]() 2h05C ![]() 2djlS 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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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 2570.447 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Solid Phase Synthesis via Phosphoramidite Chemistry |
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#2: Chemical | ChemComp-BA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% v/v MPD 40mM Sodium Cacodylate, 12mM Spermine tetra-HCI, 80 mM sodium Chloride, 20 mM Barium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2006 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→18.9 Å / Num. all: 3161 / Num. obs: 3161 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.7 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 9 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.5 / Num. unique all: 297 / % possible all: 99.3 |
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Processing
Software |
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Refinement | Starting model: PDB ENTRY 1Z7I, 2DJL Resolution: 1.6→18.9 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 421128.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.0464 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→18.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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