7YZ8
Triclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant)
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 | 2020-02-20 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9429 |
Spacegroup name | P 1 |
Unit cell lengths | 71.225, 92.571, 113.940 |
Unit cell angles | 72.87, 79.05, 67.87 |
Refinement procedure
Resolution | 48.095 - 2.500 |
R-factor | 0.1872 |
Rwork | 0.184 |
R-free | 0.24270 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4rci |
RMSD bond length | 0.010 |
RMSD bond angle | 1.173 |
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] | 49.050 | 49.050 | 2.540 |
High resolution limit [Å] | 2.500 | 13.460 | 2.500 |
Rmerge | 0.052 | 0.022 | 0.577 |
Rmeas | 0.061 | 0.028 | 0.683 |
Rpim | 0.033 | 0.016 | 0.360 |
Total number of observations | 301916 | 1509 | 15646 |
Number of reflections | 87250 | 515 | 4471 |
<I/σ(I)> | 11.2 | 32.4 | 1.6 |
Completeness [%] | 98.3 | 91.3 | 97.8 |
Redundancy | 3.5 | 2.9 | 3.5 |
CC(1/2) | 0.999 | 0.993 | 0.812 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 277 | 6-12% PEG3350, 0.2 M KSCN |