7DYX
Human JMJD5 in complex with MN and 5-((2-cyclopropylbenzyl)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 | 48.920, 64.750, 78.649 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 41.540 - 2.270 |
R-factor | 0.2436 |
Rwork | 0.242 |
R-free | 0.28010 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6f4p |
RMSD bond length | 0.004 |
RMSD bond angle | 0.583 |
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] | 48.920 | 2.410 |
High resolution limit [Å] | 2.270 | 2.270 |
Rmerge | 0.435 | 2.966 |
Number of reflections | 21676 | 215 |
<I/σ(I)> | 2.69 | 0.35 |
Completeness [%] | 97.1 | 98.2 |
Redundancy | 2.32 | |
CC(1/2) | 0.943 | 0.098 |
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 |