6E1U
Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 2: 2-[(dibenzo[b,d]furan-2-yl)oxy]-N,N-dimethylethan-1-amine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 5.0.2 |
Synchrotron site | ALS |
Beamline | 5.0.2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-11-07 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.0 |
Spacegroup name | P 63 2 2 |
Unit cell lengths | 115.361, 115.361, 58.463 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 57.681 - 1.940 |
R-factor | 0.1903 |
Rwork | 0.190 |
R-free | 0.20300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3q50 |
RMSD bond length | 0.004 |
RMSD bond angle | 1.059 |
Data reduction software | DIALS |
Data scaling software | Aimless (0.5.27) |
Phasing software | PHASER (2.7.16) |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 99.910 | 99.910 | 1.990 |
High resolution limit [Å] | 1.940 | 8.680 | 1.940 |
Rmerge | 0.095 | 0.058 | 4.303 |
Rmeas | 0.097 | 0.060 | 4.385 |
Rpim | 0.020 | 0.015 | 0.837 |
Total number of observations | 448241 | ||
Number of reflections | 17502 | 252 | 1262 |
<I/σ(I)> | 15 | ||
Completeness [%] | 100.0 | 99.8 | 100 |
Redundancy | 25.6 | 21.3 | 26.8 |
CC(1/2) | 0.999 | 0.998 | 0.698 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 294 | 0.2 M potassium sodium tartrate, 0.1 M sodium citrate (pH 5.6), 2.8 M ammonium sulfate |