1J8L
Molecular and Crystal Structure of D(CGCAAATTMO4CGCG): the Watson-Crick Type N4-Methoxycytidine/Adenosine Base Pair in B-DNA
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PHOTON FACTORY BEAMLINE BL-18B |
| Synchrotron site | Photon Factory |
| Beamline | BL-18B |
| Temperature [K] | 100 |
| Detector technology | DIFFRACTOMETER |
| Collection date | 2000-12-12 |
| Detector | WEISSENBERG |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 24.800, 40.300, 65.500 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 10.000 - 1.600 |
| R-factor | 0.218 * |
| Rwork | 0.218 |
| R-free | 0.25800 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 355d |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.900 |
| Data reduction software | MOSFLM |
| Data scaling software | CCP4 ((SCALA)) |
| Phasing software | AMoRE |
| Refinement software | CNS (1.0) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 100.000 | 1.690 |
| High resolution limit [Å] | 1.600 | 1.600 |
| Rmerge | 0.058 | 0.132 |
| Total number of observations | 62759 * | |
| Number of reflections | 7855 | |
| <I/σ(I)> | 5.5 | |
| Completeness [%] | 86.1 | 38.4 |
| Redundancy | 5.1 * |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 4 * | MPD, spermine, magnesium acetate, sodium cacodylate, sodum chloride, pH 7.0, VAPOR DIFFUSION, HANGING 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 | magnesium acetate | ||
| 4 | 1 | 1 | sodium cacodylate | ||
| 5 | 1 | 1 | sodum chloride |
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 | 10 (mM) | |
| 3 | 1 | drop | spermine tetrahydrochloride | 4.5 (mM) | |
| 4 | 1 | drop | magnesium acetate | 18 (mM) | |
| 5 | 1 | drop | MPD | 10 (%(v/v)) | |
| 6 | 1 | drop | 40 (mM) | ||
| 7 | 1 | drop | n-octyl-beta-D-glycoside | 0.1 (%) | |
| 8 | 1 | reservoir | MPD | 25 (%) |
