9KD1
Crystal structure of Bacteroides ovatus DhuD responsible for metabolism of glycosaminoglycan
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SPRING-8 BEAMLINE BL26B1 |
| Synchrotron site | SPring-8 |
| Beamline | BL26B1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-02-12 |
| Detector | DECTRIS EIGER R 4M |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 1 |
| Unit cell lengths | 71.640, 75.446, 102.068 |
| Unit cell angles | 97.69, 96.42, 95.33 |
Refinement procedure
| Resolution | 40.990 - 2.090 |
| R-factor | 0.20997 |
| Rwork | 0.208 |
| R-free | 0.25192 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.004 |
| RMSD bond angle | 1.146 |
| Data reduction software | HKL-2000 |
| Data scaling software | HKL-2000 |
| Phasing software | MOLREP |
| Refinement software | REFMAC (5.8.0430) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 40.990 | 2.140 |
| High resolution limit [Å] | 2.090 | 2.100 |
| Rmerge | 0.099 | 0.254 |
| Rmeas | 0.121 | 0.309 |
| Number of reflections | 120519 | 5925 |
| <I/σ(I)> | 14.23 | 3.55 |
| Completeness [%] | 96.7 | 85.72 |
| Redundancy | 3 | |
| CC(1/2) | 0.967 | 0.921 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | PEG 400, magnesium acetate tetrahydrate, sodium acetate |
