7PCU
Crystal structure of YTHDF1 YTH domain in complex with ebselen
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | ELETTRA BEAMLINE 11.2C |
| Synchrotron site | ELETTRA |
| Beamline | 11.2C |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-10-15 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9718 |
| Spacegroup name | P 43 21 2 |
| Unit cell lengths | 120.260, 120.260, 78.775 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 47.797 - 2.650 |
| R-factor | 0.205 |
| Rwork | 0.202 |
| R-free | 0.25220 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 4rci |
| RMSD bond length | 0.005 |
| RMSD bond angle | 0.907 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.11.1) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 47.800 | 47.800 | 2.780 |
| High resolution limit [Å] | 2.650 | 8.790 | 2.650 |
| Rmerge | 0.204 | 0.078 | 1.716 |
| Rmeas | 0.208 | 0.080 | 1.750 |
| Rpim | 0.043 | 0.018 | 0.341 |
| Total number of observations | 423712 | 10140 | 58716 |
| Number of reflections | 17368 | 558 | 2264 |
| <I/σ(I)> | 13.9 | 31.9 | 2.2 |
| Completeness [%] | 100.0 | 99.5 | 100 |
| Redundancy | 24.4 | 18.2 | 25.9 |
| CC(1/2) | 0.999 | 0.999 | 0.785 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 277 | 6% PEG3350, 0.2 M KSCN |
