+Open data
-Basic information
Entry | Database: PDB / ID: 1jrn | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Orthorhombic form of Oxytricha telomeric DNA at 2.0A | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / oxytricha / G-quartets | Function / homology | : / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | Authors | Haider, S.M. / Parkinson, G. / Neidle, S. | Citation | Journal: J.Mol.Biol. / Year: 2002 | Title: Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. Authors: Haider, S. / Parkinson, G.N. / Neidle, S. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jrn.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jrn.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 1jrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jrn_validation.pdf.gz | 394 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jrn_full_validation.pdf.gz | 395 KB | Display | |
Data in XML | 1jrn_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1jrn_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jrn ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jrn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THIS IS THE OXYTRICHA NOVA TELOMERIC SEQUENCE #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.18 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, Potassium Chloride, Magnesium Chloride, Spermine, Cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 10, 2001 |
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→50 Å / Num. all: 8736 / Num. obs: 8565 / % possible obs: 98 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.052 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.84 / % possible all: 98.2 |
Reflection | *PLUS Lowest resolution: 8 Å / % possible obs: 98 % / Redundancy: 2.08 % / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 98.2 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / σ(F): 4 / Stereochemistry target values: Engh and Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor all: 0.2753 / Rfactor obs: 0.262 / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.215 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |