8GSR
Crystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase from Sphingomonas sp. (apo-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 | 2021-10-21 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.97 |
| Spacegroup name | P 1 |
| Unit cell lengths | 64.217, 66.412, 75.202 |
| Unit cell angles | 90.15, 91.80, 104.94 |
Refinement procedure
| Resolution | 49.070 - 1.730 |
| R-factor | 0.1693 |
| Rwork | 0.168 |
| R-free | 0.20480 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | AlphaFold2 |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.854 |
| 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] | 49.070 | 49.070 | 1.760 |
| High resolution limit [Å] | 1.730 | 9.480 | 1.730 |
| Rmerge | 0.154 | 0.069 | 1.113 |
| Rmeas | 0.171 | 0.076 | 1.249 |
| Rpim | 0.075 | 0.032 | 0.559 |
| Total number of observations | 622673 | 4138 | 29475 |
| Number of reflections | 121965 | 750 | 5993 |
| <I/σ(I)> | 7 | 17.7 | 1.6 |
| Completeness [%] | 97.4 | 98.4 | 96 |
| Redundancy | 5.1 | 5.5 | 4.9 |
| CC(1/2) | 0.993 | 0.994 | 0.615 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 50% PEG 3350, 200 mM MgCl2, 100 mM Tris-HCl pH 8.5 |
