8VJT
Structure of the poly-UG quadruplex (GUGUGU)4
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 21-ID-D |
| Synchrotron site | APS |
| Beamline | 21-ID-D |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2018-11-09 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.97619 |
| Spacegroup name | P 4 21 2 |
| Unit cell lengths | 32.821, 32.821, 57.970 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 21.726 - 1.052 |
| R-factor | 0.1496 |
| Rwork | 0.148 |
| R-free | 0.16060 |
| Structure solution method | SIRAS |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.064 |
| Data reduction software | XDS (Jun 30, 2023) |
| Data scaling software | Aimless (0.7.13) |
| Phasing software | HKL2Map |
| Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 21.726 | 21.726 | 1.071 |
| High resolution limit [Å] | 1.052 | 2.855 | 1.052 |
| Rmerge | 0.077 | 0.064 | 0.803 |
| Rmeas | 0.080 | 0.067 | 0.884 |
| Rpim | 0.022 | 0.018 | 0.354 |
| Total number of observations | 191357 | 12276 | 2605 |
| Number of reflections | 14743 | 890 | 459 |
| <I/σ(I)> | 18.35 | 46.84 | 1.77 |
| Completeness [%] | 95.9 | 100 | 62.9 |
| Redundancy | 12.98 | 13.79 | 5.68 |
| CC(1/2) | 0.995 | 0.993 | 0.690 |
| Anomalous redundancy | 7.1 | 8.6 | 3.1 |
| CC(ano) | -0.294 | -0.448 | -0.003 |
| |DANO|/σ(DANO) | 0.8 | 1.0 | 0.7 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | Diffraction quality crystals were eventually obtained by sitting drop vapor diffusion by mixing 2 uL of RNA with 2 uL of crystallization reagent containing 200 mM NaCl, 100 mM bis-tris pH 6.5 and 50 % PEG 550 MME. Crystals were vitrified by direct immersion into liquid nitrogen |
