8K2E
Crystal structure of YTHDC1 and Y3 complex
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL19U1 |
Synchrotron site | SSRF |
Beamline | BL19U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-05-27 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.978 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 39.644, 103.515, 41.815 |
Unit cell angles | 90.00, 102.42, 90.00 |
Refinement procedure
Resolution | 31.710 - 1.600 |
R-factor | 0.1875 |
Rwork | 0.185 |
R-free | 0.22390 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.015 |
RMSD bond angle | 1.331 |
Data scaling software | HKL-3000 (7.21) |
Phasing software | PHASER (2.70) |
Refinement software | PHENIX (1.19.2_4158) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.630 |
High resolution limit [Å] | 1.600 | 4.340 | 1.600 |
Rmerge | 0.094 | 0.081 | 0.449 |
Rmeas | 0.102 | 0.088 | 0.494 |
Rpim | 0.039 | 0.034 | 0.200 |
Total number of observations | 291216 | ||
Number of reflections | 43363 | 2220 | 2127 |
<I/σ(I)> | 10.5 | ||
Completeness [%] | 100.0 | 99.8 | 100 |
Redundancy | 6.7 | 6.7 | 5.9 |
CC(1/2) | 0.989 | 0.992 | 0.883 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 0.1M Bis-Tris at pH 6.5, 0.2M ammonium sulfate, 25% PEG 3350 |