7YXJ
Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and 2,4-PDCA
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 | 2017-08-05 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.96863 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 53.557, 65.762, 206.957 |
Unit cell angles | 90.00, 97.78, 90.00 |
Refinement procedure
Resolution | 55.354 - 2.450 |
R-factor | 0.2073 |
Rwork | 0.206 |
R-free | 0.22970 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7yxg |
RMSD bond length | 0.006 |
RMSD bond angle | 0.778 |
Data reduction software | XDS |
Data scaling software | SCALA (3.3.22) |
Phasing software | PHASER |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 205.054 | 55.354 | 2.580 |
High resolution limit [Å] | 2.450 | 7.750 | 2.450 |
Rmeas | 0.140 | 0.064 | 1.069 |
Rpim | 0.062 | 0.028 | 0.466 |
Number of reflections | 52754 | 1740 | 7667 |
<I/σ(I)> | 7.8 | 9.6 | 1.7 |
Completeness [%] | 99.8 | 99 | 100 |
Redundancy | 4.9 | 4.6 | 5 |
CC(1/2) | 0.995 | 0.552 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.4 | 298 | Sample: 16.0 mg/ml dmJMJD7 (in 50 mM Hepes-Na pH 7.5, 200 mM NaCl, 5% glycerol), 2.0 mM MnCl2 and 4.0 mM compound. Reservoir: 0.1 M Bis-Tris pH 5.4, 0.3 M magnesium chloride, 0.1 M ammonium acetate (or alternatively, 0.1 M barium chloride), and 0.002 M manganese chloride. Cryo-protection: 20% v/v ethylene glycol. |