5VAR
Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine competitive inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 17-ID |
Synchrotron site | APS |
Beamline | 17-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-10-21 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.000 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 33.270, 39.840, 44.300 |
Unit cell angles | 90.00, 101.61, 90.00 |
Refinement procedure
Resolution | 32.590 - 1.830 |
R-factor | 0.196 |
Rwork | 0.194 |
R-free | 0.24300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2gfa |
RMSD bond length | 0.010 |
RMSD bond angle | 1.030 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.12) |
Phasing software | MOLREP |
Refinement software | BUSTER (2.11.7) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 39.840 | 39.840 | 1.930 |
High resolution limit [Å] | 1.830 | 5.780 | 1.830 |
Rmerge | 0.086 | 0.052 | 0.654 |
Rmeas | 0.099 | 0.061 | 0.763 |
Rpim | 0.049 | 0.030 | 0.386 |
Total number of observations | 38231 | ||
Number of reflections | 9890 | ||
<I/σ(I)> | 10.7 | ||
Completeness [%] | 97.2 | 98.1 | 95.2 |
Redundancy | 3.9 | 3.6 | 3.7 |
CC(1/2) | 0.997 | 0.998 | 0.731 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | 18%(w/v) PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5 |