4Y1M
An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state
Experimental procedure
Experimental method | MAD |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 80 |
Detector technology | PIXEL |
Collection date | 2014-06-22 |
Detector | PSI PILATUS 6M |
Wavelength(s) | 0.769, 0.7692, 0.9999 |
Spacegroup name | H 3 2 |
Unit cell lengths | 159.384, 159.384, 277.108 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 123.600 - 3.000 |
R-factor | 0.2186 |
Rwork | 0.217 |
R-free | 0.25210 |
Structure solution method | MAD |
RMSD bond length | 0.002 |
RMSD bond angle | 0.614 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | SHELX |
Refinement software | PHENIX ((phenix.refine: dev_1834)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 123.600 | 3.110 |
High resolution limit [Å] | 3.000 | 3.000 |
Rmerge | 0.116 | 1.010 |
Number of reflections | 27410 | |
<I/σ(I)> | 20.2 | 2.41 |
Completeness [%] | 100.0 | 100 |
Redundancy | 11.3 | 11.6 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 294 | 0.2 mM RNA in 10 mm NaCacodylate, 50 mM NaCl, 10 mM MgCl2 with a mother liquor of 10% MPD, 40 mM Na cacodylate pH 7, 80 mM SrCl2, 20 mM MgCl2, 12 mM spermine tetra-HCl at 21 C. Native crystals were quickly cryo-protected in mother liquor plus 20% ethylene glycol prior to flash freezing in liquid N2. |