4WQN
Crystal structure of N6-methyladenosine RNA reader YTHDF2
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL17U |
Synchrotron site | SSRF |
Beamline | BL17U |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2014-06-23 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.97915 |
Spacegroup name | P 65 |
Unit cell lengths | 76.689, 76.689, 131.241 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 38.344 - 2.121 |
R-factor | 0.1878 |
Rwork | 0.186 |
R-free | 0.22140 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2yu6 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.043 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Refinement software | PHENIX ((phenix.refine: 1.8.2_1309)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.200 |
High resolution limit [Å] | 2.120 | 4.570 | 2.120 |
Rmerge | 0.113 | 0.059 | 0.898 |
Rmeas | 0.119 | 0.062 | 0.949 |
Rpim | 0.037 | 0.019 | 0.302 |
Total number of observations | 259897 | ||
Number of reflections | 24685 | ||
<I/σ(I)> | 9 | ||
Completeness [%] | 100.0 | 99.9 | 100 |
Redundancy | 10.5 | 10.4 | 9.5 |
CC(1/2) | 0.998 | 0.893 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.3 | 277 | 0.1M phosphate-citric pH 4.3, 0.2M Lithium Sulfate, 10% PEG8000 |