5DGH
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5
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 | 2015-06-12 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 87.900, 110.340, 41.253 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.040 - 2.100 |
R-factor | 0.18945 |
Rwork | 0.187 |
R-free | 0.23140 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 3t7a |
RMSD bond length | 0.009 |
RMSD bond angle | 1.450 |
Data scaling software | HKL-2000 |
Refinement software | REFMAC (5.7.0032) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.350 |
High resolution limit [Å] | 2.100 | 2.100 |
Rmerge | 0.382 | |
Number of reflections | 23365 | |
<I/σ(I)> | 16.5 | 2.5 |
Completeness [%] | 96.8 | 87.2 |
Redundancy | 4.8 | 3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight. The crystals were soaked under the above stabilizing buffer for three days with 2 mM compound. |