7AG6
Crystal structure of SF kinase YihV from E. coli in complex with sulfofructose (SF), ADP-Mg
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-07-21 |
Detector | DECTRIS EIGER2 XE 16M |
Wavelength(s) | 0.97625 |
Spacegroup name | P 32 2 1 |
Unit cell lengths | 94.880, 94.880, 167.430 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 46.170 - 2.080 |
R-factor | 0.2028 |
Rwork | 0.201 |
R-free | 0.23740 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1rkd |
RMSD bond length | 0.009 |
RMSD bond angle | 1.487 |
Data reduction software | xia2 |
Data scaling software | Aimless (0.7.1) |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0266) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 46.170 | 46.170 | 2.130 |
High resolution limit [Å] | 2.080 | 9.300 | 2.080 |
Rmerge | 0.104 | 0.030 | 1.963 |
Rmeas | 0.108 | 0.032 | 2.047 |
Rpim | 0.031 | 0.010 | 0.573 |
Total number of observations | 622973 | 6521 | 47725 |
Number of reflections | 53073 | 685 | 3869 |
<I/σ(I)> | 14.6 | 52 | 1.2 |
Completeness [%] | 99.8 | 99.3 | 99.9 |
Redundancy | 11.7 | 9.5 | 12.3 |
CC(1/2) | 0.999 | 1.000 | 0.616 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 25% PEG 1500 w/v, 0.1 M MIB (malonic acid, imidazole, boric acid) buffer pH 5 |