7DYU
Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I24 |
Synchrotron site | Diamond |
Beamline | I24 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-11-28 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.96862 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 49.372, 64.564, 78.486 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.860 - 1.720 |
R-factor | 0.1612 |
Rwork | 0.160 |
R-free | 0.19460 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6f4p |
RMSD bond length | 0.017 |
RMSD bond angle | 1.271 |
Data reduction software | XDS |
Data scaling software | STARANISO |
Phasing software | PHASER |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 49.860 | 1.850 |
High resolution limit [Å] | 1.720 | 1.720 |
Rmerge | 0.155 | 1.805 |
Number of reflections | 38768 | 1040 |
<I/σ(I)> | 11.9 | 1.2 |
Completeness [%] | 94.2 | 58.5 |
Redundancy | 12.4 | 8.4 |
CC(1/2) | 0.996 | 0.351 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride |