363D
High-resolution crystal structure of a fully modified N3'-> P5' phosphoramidate DNA dodecamer duplex
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | ROTATING ANODE |
| Temperature [K] | 290 |
| Detector technology | IMAGE PLATE |
| Collection date | 1996-04-01 |
| Detector | RIGAKU RAXIS II |
| Spacegroup name | H 3 2 |
| Unit cell lengths | 40.150, 40.150, 304.210 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 8.000 - 2.000 |
| R-factor | 0.192 |
| Rwork | 0.192 |
| R-free | 0.24700 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | A-FORM DUPLEX |
| RMSD bond length | 0.010 * |
| RMSD bond angle | 1.350 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | AMoRE |
| Refinement software | X-PLOR |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 34.000 | |
| High resolution limit [Å] | 2.000 | 2.000 |
| Rmerge | 0.082 | |
| Total number of observations | 76542 * | |
| Number of reflections | 6737 | |
| Completeness [%] | 98.4 | |
| Redundancy | 11.4 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion, sitting drop * | 7 | 293 | pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | WATER | ||
| 10 | 1 | 2 | 1,6-HEXANEDIOL | ||
| 2 | 1 | 1 | NH4CL | ||
| 3 | 1 | 1 | MGCL2 | ||
| 4 | 1 | 1 | NA HEPES | ||
| 5 | 1 | 1 | 1,6-HEXANEDIOL | ||
| 6 | 1 | 2 | WATER | ||
| 7 | 1 | 2 | NH4CL | ||
| 8 | 1 | 2 | MGCL2 | ||
| 9 | 1 | 2 | NA HEPES |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | phosphoramidate dodecamer | 1.5 (mM) | |
| 2 | 1 | drop | sodium cacodylate | 40 (mM) | |
| 3 | 1 | drop | 10-500 (mM) | can be replaced by CaCl2 | |
| 4 | 1 | drop | spermine tetrahydrochloride | 1-30 (mM) | |
| 5 | 1 | reservoir | MPD | 20-40 (%) |
