6YDJ
P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with glucose 6-phosphate and trifluoromagnesate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-02-10 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.91587 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 37.080, 54.250, 104.320 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 52.210 - 1.040 |
R-factor | 0.1506 |
Rwork | 0.150 |
R-free | 0.16850 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2wf5 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.473 |
Data reduction software | XDS |
Data scaling software | xia2 |
Phasing software | PHASER (2.6.1) |
Refinement software | REFMAC (5.8.0189) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 54.250 | 54.320 | 1.060 |
High resolution limit [Å] | 1.040 | 2.820 | 1.040 |
Rmerge | 0.067 | 1.138 | |
Rmeas | 0.073 | 0.036 | 1.295 |
Rpim | 0.028 | 0.014 | 0.609 |
Number of reflections | 101730 | 5462 | 5021 |
<I/σ(I)> | 12.4 | 46.5 | 1.1 |
Completeness [%] | 99.9 | 100 | 99.3 |
Redundancy | 6.7 | 6.9 | 4.4 |
CC(1/2) | 0.999 | 1.000 | 0.544 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 290 | PEG 4000 (32% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (13 mM), magnesium chloride (5 mM), EDTA (200 uM), sodium azide (500 uM), sodium fluoride (15 mM), glucose 6-phosphate (10 mM), beta-phosphoglucomutase (0.4 mM) |