7AT9
Structure of protein kinase ck2 catalytic subunit (csnk2a2 gene product) in complex with the ATP-competitive inhibitor MB002 and the alphaD-pocket ligand 3,4-dichlorophenethylamine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the alphaD-pocket ligand 3,4-dichlorophenethylamine was introduced by extensive soaking. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 48.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.482 | α = 66.614 |
b = 47.661 | β = 89.437 |
c = 50.733 | γ = 88.659 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 X 2M | 2018-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.873127 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||
1 | 1.039 | 46.565 | 80.1 | 0.075 | 0.075 | 0.079 | 0.025 | 0.999 | 13.4 | 8.6 | 154027 | 11.45 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.039 | 1.103 | 24.5 | 1.096 | 1.096 | 1.239 | 0.558 | 0.513 | 1.2 | 4.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | AB INITIO PHASING | FREE R-VALUE | 1.05 | 43.74 | 1.96 | 153804 | 1555 | 81.24 | 0.1293 | 0.1291 | 0.1496 | 19.12 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.471 |
f_angle_d | 1.1633 |
f_chiral_restr | 0.0931 |
f_bond_d | 0.0102 |
f_plane_restr | 0.0089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2764 |
Nucleic Acid Atoms | |
Solvent Atoms | 390 |
Heterogen Atoms | 71 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
Arcimboldo | phasing |
PHENIX | model building |
PHENIX | refinement |