3CJZ
Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m22G:A pairs
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 22-BM |
| Synchrotron site | APS |
| Beamline | 22-BM |
| Temperature [K] | 120 |
| Detector technology | CCD |
| Collection date | 2004-11-09 |
| Detector | MARMOSAIC 225 mm CCD |
| Wavelength(s) | 1.00 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 58.118, 25.970, 45.393 |
| Unit cell angles | 90.00, 97.41, 90.00 |
Refinement procedure
| Resolution | 44.990 - 1.800 |
| R-factor | 0.19938 |
| Rwork | 0.190 |
| R-free | 0.27742 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | A cononical A-RNA dodecamer generated with the program TURBO-FRODO omitting U13 and U26. |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.356 |
| Data reduction software | X-GEN |
| Data scaling software | X-GEN |
| Phasing software | MOLREP ((CCP4)) |
| Refinement software | REFMAC (5.2.0003) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 44.990 | 1.860 |
| High resolution limit [Å] | 1.800 | 1.800 |
| Rmerge | 0.099 | 0.354 |
| Number of reflections | 6027 | |
| <I/σ(I)> | 26.4 | 4.8 |
| Completeness [%] | 93.9 | 81.4 |
| Redundancy | 2 | 1.9 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 301 | 2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a reservoir of 1ml of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 301K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | 5% MPD | ||
| 2 | 1 | 1 | sodium cacodylate | ||
| 3 | 1 | 1 | spermine-4HCl | ||
| 4 | 1 | 1 | sodium chloride | ||
| 5 | 1 | 2 | 35% MPD |
