6VMY
Structure of the B. subtilis cobalamin riboswitch
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2013-06-03 |
Detector | RAYONIX MX-225 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 65 2 2 |
Unit cell lengths | 118.282, 118.282, 261.547 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 39.210 - 3.250 |
Rwork | 0.263 |
R-free | 0.27900 |
Structure solution method | MIRAS |
RMSD bond length | 0.003 |
RMSD bond angle | 0.807 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | SHARP |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 39.213 | 3.460 |
High resolution limit [Å] | 3.253 | 3.280 |
Rmerge | 0.160 | 4.129 |
Rmeas | 0.162 | 4.168 |
Rpim | 0.025 | 0.561 |
Number of reflections | 15338 | 41046 |
<I/σ(I)> | 18.2 | |
Completeness [%] | 92.8 | 43.8 |
Redundancy | 47 | 54 |
CC(1/2) | 0.996 | 0.598 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 287 | Purified RNA was incubated at room temperature for 30 minutes in 25 mM Tris-HCl, pH 8.0, 50 mM potassium chloride, 10 mM magnesium chloride, 0.5 mM adenosylcobalamin prior to crystallization in 50 mM sodium cacodylate, 15% (v/v) PEG 400, 0.2 mM cobalt hexamine, 80 mM magnesium acetate, 1 mM spermine between pH 6.0 to pH 6.5 at 14C by vapor diffusion in a hanging drop format |