8PPF
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4-trisphosphate/AMP-PNP/Mg
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALBA BEAMLINE XALOC |
Synchrotron site | ALBA |
Beamline | XALOC |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-06-19 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.979264 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 72.815, 97.587, 191.929 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.840 - 1.850 |
R-factor | 0.19735 |
Rwork | 0.196 |
R-free | 0.22779 |
Structure solution method | FOURIER SYNTHESIS |
RMSD bond length | 0.005 |
RMSD bond angle | 1.356 |
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] | 48.840 | 1.890 |
High resolution limit [Å] | 1.850 | 1.850 |
Rpim | 0.040 | 0.263 |
Number of reflections | 56714 | 2593 |
<I/σ(I)> | 12 | 2.2 |
Completeness [%] | 96.8 | 74.3 |
Redundancy | 10.5 | 7.2 |
CC(1/2) | 0.994 | 0.779 |
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: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MgCl2. |