8Q9S
STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR SGC-CK2-1
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-04-17 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.97624 |
Spacegroup name | P 1 |
Unit cell lengths | 46.217, 47.682, 50.562 |
Unit cell angles | 66.83, 89.43, 88.93 |
Refinement procedure
Resolution | 32.720 - 1.352 |
R-factor | 0.1366 |
Rwork | 0.135 |
R-free | 0.16880 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.008 |
RMSD bond angle | 0.886 |
Phasing software | PHENIX (1.20.1_4487) |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 46.483 | 1.519 |
High resolution limit [Å] | 1.352 | 1.352 |
Rmerge | 0.097 | 1.482 |
Rmeas | 0.104 | 1.598 |
Rpim | 0.057 | 0.594 |
Number of reflections | 56703 | 2835 |
<I/σ(I)> | 7.8 | 1.6 |
Completeness [%] | 65.3 | 11.1 |
Redundancy | 7.2 | 7.1 |
CC(1/2) | 0.997 | 0.589 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. A CRYSTAL WAS PURGED TWICE WITH RESERVOIR SOLUTION BEFORE ADDING SGC-CK2-1 (10 MM IN DMSO) TO A FINAL CONCENTRATION OF 2.5 MM TO THE CRYSTAL MOTHOR LIQUOR FOR EXTENSIVE SOAKING AND REPLACEMENT OF THE INITIAL INHIBITOR MB002 BY SGC-CK2-1. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K. |