8GST
Crystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase from Sphingomonas sp. (pyruvate bound-form)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SPRING-8 BEAMLINE BL45XU |
| Synchrotron site | SPring-8 |
| Beamline | BL45XU |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-11-15 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 1 |
| Unit cell lengths | 64.254, 66.228, 75.256 |
| Unit cell angles | 90.27, 91.43, 105.20 |
Refinement procedure
| Resolution | 48.988 - 1.710 |
| R-factor | 0.1814 |
| Rwork | 0.180 |
| R-free | 0.21820 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 8gsr |
| RMSD bond length | 0.006 |
| RMSD bond angle | 0.860 |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.12_2829) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 48.990 | 48.990 | 1.740 |
| High resolution limit [Å] | 1.710 | 9.370 | 1.710 |
| Rmerge | 0.150 | 0.053 | 1.220 |
| Rmeas | 0.171 | 0.059 | 1.350 |
| Rpim | 0.080 | 0.025 | 0.573 |
| Total number of observations | 623308 | 4094 | 33385 |
| Number of reflections | 125104 | 778 | 6159 |
| <I/σ(I)> | 12.6 | 32.3 | 2.5 |
| Completeness [%] | 96.7 | 98.9 | 95.8 |
| Redundancy | 5 | 5.3 | 5.4 |
| CC(1/2) | 0.974 | 0.996 | 0.737 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 50% PEG 3350, 200 mM MgCl2, 100 mM Tris-HCl pH 8.5 |
