6S0V
The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, neamine and sulfate
Experimental procedure
| Experimental method | MAD |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 21-ID-D |
| Synchrotron site | APS |
| Beamline | 21-ID-D |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2018-07-27 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.97938 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 50.467, 185.250, 110.460 |
| Unit cell angles | 90.00, 94.68, 90.00 |
Refinement procedure
| Resolution | 48.540 - 3.000 |
| R-factor | 0.20112 |
| Rwork | 0.200 |
| R-free | 0.22824 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 6s0t |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.351 |
| 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] | 48.540 | 3.050 |
| High resolution limit [Å] | 3.000 | 3.000 |
| Rmerge | 0.126 | 0.947 |
| Number of reflections | 40424 | 2006 |
| <I/σ(I)> | 6.6 | |
| Completeness [%] | 90.7 | |
| Redundancy | 5.2 | |
| CC(1/2) | 0.982 | 0.661 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | 1:1 of 28% PEG4000 (w/v), 0.5 M lithium sulfate, 0.1 M HEPES, 0.1 M sodium acetate and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl; soaked with 0.02 M neamine |
