7DYT
Human JMJD5 in complex with MN and 5-((4-methoxybenzyl)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 | 49.350, 65.000, 78.610 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 41.800 - 1.620 |
R-factor | 0.1638 |
Rwork | 0.163 |
R-free | 0.18900 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6f4p |
RMSD bond length | 0.005 |
RMSD bond angle | 0.763 |
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] | 50.090 | 1.650 |
High resolution limit [Å] | 1.620 | 1.620 |
Rmerge | 0.161 | 1.117 |
Number of reflections | 30389 | 965 |
<I/σ(I)> | 11.2 | 1.1 |
Completeness [%] | 92.5 | 59.2 |
Redundancy | 10.3 | 3.9 |
CC(1/2) | 0.996 | 0.451 |
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 |