6S0U
The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel and 2-oxoglutarate
Experimental procedure
Experimental method | MAD |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-ID |
Synchrotron site | APS |
Beamline | 19-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-06-30 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97930 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 49.825, 183.691, 110.169 |
Unit cell angles | 90.00, 96.55, 90.00 |
Refinement procedure
Resolution | 45.730 - 2.150 |
R-factor | 0.1982 |
Rwork | 0.196 |
R-free | 0.24429 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6s0t |
RMSD bond length | 0.010 |
RMSD bond angle | 1.540 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | HKL-3000 |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 45.730 | 2.190 |
High resolution limit [Å] | 2.140 | 2.150 |
Rmerge | 0.179 | 0.690 |
Number of reflections | 105045 | 5177 |
<I/σ(I)> | 6.2 | |
Completeness [%] | 92.2 | |
Redundancy | 3.9 | |
CC(1/2) | 0.579 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | 1:1 of 25% PEG4000, 0.2 M alpha-Ketoglutaric acid disodium salt dihydrate, 0.05 M bis-tris methane, 0.15 M NaCl and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl |