6LD0
Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic isofagomine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSRRC BEAMLINE BL15A1 |
Synchrotron site | NSRRC |
Beamline | BL15A1 |
Temperature [K] | 110 |
Detector technology | CCD |
Collection date | 2013-10-05 |
Detector | RAYONIX MX300HE |
Wavelength(s) | 1 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 92.914, 105.395, 162.293 |
Unit cell angles | 90.00, 91.16, 90.00 |
Refinement procedure
Resolution | 20.194 - 1.901 |
R-factor | 0.2012 |
Rwork | 0.201 |
R-free | 0.23490 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3k46 |
RMSD bond length | 0.004 |
RMSD bond angle | 1.003 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX |
Refinement software | PHENIX (1.8.2_1309) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 30.000 | 30.000 | 1.970 |
High resolution limit [Å] | 1.900 | 4.090 | 1.900 |
Rmerge | 0.077 | 0.018 | 0.446 |
Rmeas | 0.089 | 0.021 | 0.513 |
Rpim | 0.044 | 0.011 | 0.250 |
Total number of observations | 980607 | ||
Number of reflections | 241740 | 24570 | 24343 |
<I/σ(I)> | 9.5 | ||
Completeness [%] | 98.7 | 98.8 | 99.8 |
Redundancy | 4.1 | 3.8 | 4.1 |
CC(1/2) | 0.999 | 0.881 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 0.1 M sodium cacodylate, pH 6.5, 8% w/v PEG 20K |