8YAM
Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL45XU |
Synchrotron site | SPring-8 |
Beamline | BL45XU |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-04-06 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.0 |
Spacegroup name | P 63 2 2 |
Unit cell lengths | 115.880, 115.880, 58.260 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 41.100 - 2.150 |
Rwork | 0.184 |
R-free | 0.19300 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.005 |
RMSD bond angle | 0.983 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (v1.17.1-3660) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 41.100 | 2.280 |
High resolution limit [Å] | 2.150 | 2.150 |
Rmerge | 0.083 | 3.360 |
Rpim | 0.015 | 0.585 |
Number of reflections | 12994 | 2040 |
<I/σ(I)> | 29.8 | 1.57 |
Completeness [%] | 99.6 | 99.2 |
Redundancy | 33.2 | 33.3 |
CC(1/2) | 0.999 | 0.595 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 0.3M potassium sodium tartrate, 0.1M sodium citrate (pH 5.6), 2.2M ammonium sulfate |