6M88
Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with myricetin
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 22-ID |
Synchrotron site | APS |
Beamline | 22-ID |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2018-04-12 |
Detector | RAYONIX MX300-HS |
Wavelength(s) | 1 |
Spacegroup name | P 42 21 2 |
Unit cell lengths | 77.717, 77.717, 84.465 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 1.900 |
R-factor | 0.17689 |
Rwork | 0.173 |
R-free | 0.24428 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 5w2g |
RMSD bond length | 0.009 |
RMSD bond angle | 1.310 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Refinement software | REFMAC (5.8.0189) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.930 |
High resolution limit [Å] | 1.900 | 1.900 |
Rmerge | 0.123 | 0.728 |
Rmeas | 0.130 | 0.768 |
Rpim | 0.040 | 0.241 |
Number of reflections | 20939 | 1023 |
<I/σ(I)> | 16.9 | 4 |
Completeness [%] | 99.6 | 100 |
Redundancy | 9.7 | 9.6 |
CC(1/2) | 0.977 | 0.880 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 2 mM myricetin for 3 days. |