7DYW
Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE MASSIF-1 |
Synchrotron site | ESRF |
Beamline | MASSIF-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-11-03 |
Detector | DECTRIS PILATUS3 2M |
Wavelength(s) | 0.965459 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 49.642, 65.415, 79.566 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 42.120 - 2.130 |
R-factor | 0.2154 |
Rwork | 0.214 |
R-free | 0.23920 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6f4p |
RMSD bond length | 0.012 |
RMSD bond angle | 0.940 |
Data reduction software | XDS |
Data scaling software | pointless |
Phasing software | PHASER |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 42.120 | 2.260 |
High resolution limit [Å] | 2.130 | 2.130 |
Rmerge | 0.202 | 2.864 |
Number of reflections | 27195 | 1249 |
<I/σ(I)> | 6 | 0.43 |
Completeness [%] | 97.3 | 92.6 |
Redundancy | 2.81 | |
CC(1/2) | 0.991 | 0.129 |
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 |