6M8D
Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with diosmetin
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 22-BM |
Synchrotron site | APS |
Beamline | 22-BM |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-10-20 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 1 |
Spacegroup name | P 42 21 2 |
Unit cell lengths | 77.971, 77.971, 85.362 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 38.000 - 2.000 |
R-factor | 0.17644 |
Rwork | 0.173 |
R-free | 0.23949 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 5w2g |
RMSD bond length | 0.007 |
RMSD bond angle | 1.208 |
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 | 2.030 |
High resolution limit [Å] | 2.000 | 2.000 |
Rmerge | 0.090 | 0.896 |
Rmeas | 0.096 | 0.955 |
Rpim | 0.032 | 0.317 |
Number of reflections | 18315 | 877 |
<I/σ(I)> | 22.3 | 2.8 |
Completeness [%] | 99.5 | 100 |
Redundancy | 7.8 | 8 |
CC(1/2) | 0.786 |
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 10 mM diosmetin for 3 days. |