1G8V
MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PHOTON FACTORY BEAMLINE BL-6B |
| Synchrotron site | Photon Factory |
| Beamline | BL-6B |
| Temperature [K] | 100 |
| Detector technology | DIFFRACTOMETER |
| Collection date | 2000-01-23 |
| Detector | WEISSENBERG |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 25.300, 41.700, 66.000 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 50.000 - 1.800 |
| R-factor | 0.208 * |
| Rwork | 0.208 |
| R-free | 0.23900 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 355d |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.900 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | AMoRE |
| Refinement software | CNS (1.0) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 1.860 |
| High resolution limit [Å] | 1.800 | 1.800 |
| Rmerge | 0.028 | 0.243 |
| Total number of observations | 45728 * | |
| Number of reflections | 6948 | |
| Completeness [%] | 99.3 | 97.3 |
| Redundancy | 6.58 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion, hanging drop * | 6 | 277 | MPD, spermine, sodium chloride, potassium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | MPD | ||
| 2 | 1 | 1 | spermine | ||
| 3 | 1 | 1 | NaCl | ||
| 4 | 1 | 1 | KCl | ||
| 5 | 1 | 1 | cacodylate | ||
| 6 | 1 | 2 | MPD |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | DNA | 0.5 (mM) | |
| 2 | 1 | drop | sodium cacodylate | 20 (mM) | |
| 3 | 1 | drop | spermine tetra-HCl | 6 (mM) | |
| 4 | 1 | drop | 6 (mM) | ||
| 5 | 1 | drop | 40 (mM) | ||
| 6 | 1 | drop | 5 (%) | ||
| 7 | 1 | reservoir | MPD | 40 (%) |
