1MDG
An Alternating Antiparallel Octaplex in an RNA Crystal Structure
Experimental procedure
| Experimental method | MAD |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 14-BM-D |
| Synchrotron site | APS |
| Beamline | 14-BM-D |
| Temperature [K] | 105 |
| Detector technology | CCD |
| Collection date | 2001-05-31 |
| Detector | ENRAF-NONIUS |
| Wavelength(s) | 0.9195, 0.9192, 0.800 |
| Spacegroup name | I 4 2 2 |
| Unit cell lengths | 35.956, 35.956, 38.045 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 30.000 - 1.500 |
| Rwork | 0.172 |
| R-free | 0.19400 |
| Structure solution method | MAD |
| RMSD bond length | 0.010 * |
| RMSD bond angle | 4.600 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | CNS |
| Refinement software | CNS |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 30.000 | 1.550 |
| High resolution limit [Å] | 1.500 | 1.500 |
| Rmerge | 0.056 * | |
| Total number of observations | 158438 * | |
| Number of reflections | 3800 | |
| Completeness [%] | 99.8 | 98.6 |
| Redundancy | 41.7 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.6 | 293 | MPD, MgCl2, Cobalt(III)hexammine, ethidine bromide, sodium cacodylate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | MPD | ||
| 2 | 1 | 1 | MgCl2 | ||
| 3 | 1 | 1 | Cobalt(III)hexammine | ||
| 4 | 1 | 1 | ethidine bromide | ||
| 5 | 1 | 1 | sodium cacodylate |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | RNA | 1 (mM) | |
| 2 | 1 | drop | sodium cacodylate | 40 (mM) | pH6.6 |
| 3 | 1 | drop | 5 (mM) | ||
| 4 | 1 | drop | cobalt hexammine chloride | 1 (mM) | |
| 5 | 1 | drop | ethidine bromide | 1 (mM) | |
| 6 | 1 | drop | MPD | 2 (%(v/v)) | |
| 7 | 1 | reservoir | MPD | 15 (%) |
