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 |