6JW8
The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin B
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PHOTON FACTORY BEAMLINE BL-5A |
| Synchrotron site | Photon Factory |
| Beamline | BL-5A |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2018-01-28 |
| Detector | ADSC QUANTUM 315r |
| Wavelength(s) | 1.0000 |
| Spacegroup name | P 31 2 1 |
| Unit cell lengths | 119.761, 119.761, 132.904 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 44.340 - 2.400 |
| R-factor | 0.22163 |
| Rwork | 0.220 |
| R-free | 0.25190 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 4h3v |
| RMSD bond length | 0.017 |
| RMSD bond angle | 1.995 |
| Data reduction software | HKL-2000 |
| Data scaling software | SCALEPACK |
| Phasing software | MOLREP |
| Refinement software | REFMAC (5.7.0029) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 2.440 |
| High resolution limit [Å] | 2.400 | 2.400 |
| Rmerge | 0.082 | 0.713 |
| Number of reflections | 43656 | 2141 |
| <I/σ(I)> | 31.5 | 2.5 |
| Completeness [%] | 100.0 | 99.5 |
| Redundancy | 9.9 | 7.9 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | PEG 8000, imidazole, calcium acetate, NADH, 3"-deamino-3"-hydroxykanamycin B |
