6S0S
The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, ribostamycin B 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 | 50.083, 184.582, 110.333 |
| Unit cell angles | 90.00, 94.97, 90.00 |
Refinement procedure
| Resolution | 47.270 - 2.400 |
| R-factor | 0.17437 |
| Rwork | 0.173 |
| R-free | 0.20420 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 6s0t |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.455 |
| 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] | 47.270 | 2.540 |
| High resolution limit [Å] | 2.400 | 2.500 |
| Rmerge | 0.098 | 0.863 |
| Number of reflections | 67239 | 3220 |
| <I/σ(I)> | 7.3 | |
| Completeness [%] | 91.1 | |
| Redundancy | 6.9 | |
| CC(1/2) | 0.993 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | 1:1 of 28% PEG4000 (w/v), 0.2 M a-ketoglutaric acid disodium salt dihydrate, 0.1 M HEPES, and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl |
