8PPA
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn
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 | 72.653, 97.919, 192.066 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.910 - 1.730 |
R-factor | 0.19464 |
Rwork | 0.193 |
R-free | 0.21823 |
Structure solution method | FOURIER SYNTHESIS |
RMSD bond length | 0.006 |
RMSD bond angle | 1.402 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | REFMAC |
Refinement software | REFMAC (v5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 49.860 | 1.760 |
High resolution limit [Å] | 1.730 | 1.730 |
Rpim | 0.037 | 0.417 |
Number of reflections | 64275 | 3876 |
<I/σ(I)> | 12.1 | 1.8 |
Completeness [%] | 89.5 | 100 |
Redundancy | 11.8 | 12.2 |
CC(1/2) | 0.994 | 0.756 |
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 MnCl2. |