4Q4C
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and synthetic 1,5-(PP)2-IP4 (1,5-IP8)
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 | 2014-03-15 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 89.519, 110.224, 41.381 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 46.980 - 1.900 |
R-factor | 0.16346 |
Rwork | 0.162 |
R-free | 0.19211 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 3t9f |
RMSD bond length | 0.010 |
RMSD bond angle | 1.566 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | CCP4 |
Refinement software | REFMAC (5.7.0032) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.930 |
High resolution limit [Å] | 1.900 | 1.900 |
Number of reflections | 33191 | |
<I/σ(I)> | 22.2 | 3 |
Completeness [%] | 99.2 | 95.9 |
Redundancy | 4.9 | 3.1 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 12% w/v PEG3350, 20 mM magnesium chloride, 0.1 M HEPES, pH 7.0, 1 mM ATP, 2 mM cadmium chloride, crystals transferred to stabilizing buffer (22% w/v PEG3350, 10 mM magnesium chloride, 0.1 M sodium acetate, pH 5.2) at 277 K overnight (ATP in the crystals was hydrolyzed to ADP) then soaked for three days in stabilizing buffer containing 2 mM 1,5-IP8, VAPOR DIFFUSION, HANGING DROP |