5BYA
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PCP)2-IP4
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 | 2015-04-10 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 88.567, 110.400, 41.455 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 35.570 - 1.900 |
R-factor | 0.1448 |
Rwork | 0.141 |
R-free | 0.19900 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 3t7a |
RMSD bond length | 0.007 |
RMSD bond angle | 1.327 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHASER |
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 |
Rmerge | 0.668 | |
Number of reflections | 32965 | |
<I/σ(I)> | 15.76 | 2.42 |
Completeness [%] | 99.9 | 99.9 |
Redundancy | 6.6 | 6.3 |
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 ATP 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, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog. |