8PPG
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID23-1 |
Synchrotron site | ESRF |
Beamline | ID23-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-07-23 |
Detector | DECTRIS EIGER2 X CdTe 16M |
Wavelength(s) | 0.8856 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 71.283, 97.102, 190.755 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 95.380 - 1.750 |
R-factor | 0.20785 |
Rwork | 0.206 |
R-free | 0.24350 |
Structure solution method | FOURIER SYNTHESIS |
RMSD bond length | 0.008 |
RMSD bond angle | 1.442 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 190.760 | 1.780 |
High resolution limit [Å] | 1.750 | 1.750 |
Rpim | 0.024 | 0.572 |
Number of reflections | 67053 | 3682 |
<I/σ(I)> | 13.6 | 1.3 |
Completeness [%] | 100.0 | 100 |
Redundancy | 13.2 | 13.6 |
CC(1/2) | 0.999 | 0.676 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | 0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosyl 1,3,4-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2. |