6VI7
Probing extradiol dioxygenase mechanism in NAD(+) biosynthesis by viewing reaction cycle intermediates - a substrate bidentately bound structure
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 19-BM |
| Synchrotron site | APS |
| Beamline | 19-BM |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2017-11-14 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.97919 |
| Spacegroup name | P 65 2 2 |
| Unit cell lengths | 58.040, 58.040, 231.580 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 37.955 - 2.617 |
| R-factor | 0.2077 |
| Rwork | 0.199 |
| R-free | 0.28950 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1yfu |
| RMSD bond length | 0.014 |
| RMSD bond angle | 1.290 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | PHENIX |
| Refinement software | PHENIX (1.16) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 50.000 | 50.000 | 2.660 |
| High resolution limit [Å] | 2.610 | 7.080 | 2.610 |
| Rmerge | 0.221 | 0.106 | 1.224 |
| Rmeas | 0.226 | 0.109 | 1.248 |
| Rpim | 0.045 | 0.025 | 0.241 |
| Total number of observations | 196633 | ||
| Number of reflections | 7721 | 471 | 374 |
| <I/σ(I)> | 4.3 | ||
| Completeness [%] | 99.7 | 95.3 | 100 |
| Redundancy | 25.5 | 19.2 | 26.3 |
| CC(1/2) | 0.988 | 0.984 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 15% PEG8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride, pH 8.5 |
