4Q4D
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and synthetic 3,5-(PP)2-IP4 (3,5-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 | 88.790, 110.681, 41.379 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 47.010 - 1.850 |
| R-factor | 0.1819 |
| Rwork | 0.180 |
| R-free | 0.21584 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 3t9f |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.580 |
| 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 | 1.880 |
| High resolution limit [Å] | 1.850 | 1.850 |
| Number of reflections | 35810 | |
| <I/σ(I)> | 25.7 | 3 |
| Completeness [%] | 99.7 | 96.3 |
| Redundancy | 6.6 | 4.3 |
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 AMP-PNP, 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 3,5-IP8, VAPOR DIFFUSION, HANGING DROP |
