5D6X
Crystal structure of double tudor domain of human lysine demethylase KDM4A
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2014-10-23 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.979 |
Spacegroup name | I 21 3 |
Unit cell lengths | 134.829, 134.829, 134.829 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 42.600 - 2.153 |
R-factor | 0.1622 |
Rwork | 0.159 |
R-free | 0.19970 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.106 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHENIX |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 42.600 | 2.280 | |
High resolution limit [Å] | 2.150 | 6.410 | 2.150 |
Rmerge | 0.073 | 0.042 | 0.448 |
Rmeas | 0.079 | 0.045 | 0.484 |
Total number of observations | 306499 | ||
Number of reflections | 42897 | 1630 | 6933 |
<I/σ(I)> | 17.97 | 40.51 | 4.38 |
Completeness [%] | 100.0 | 99.6 | 99.9 |
Redundancy | 7.14 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium sulfate, 1% w/v peg3350 and 0.1M Bis-Tris pH5.5) Cryoprotected with additional 20% glycerol |