7AT5
Structure of protein kinase ck2 catalytic subunit (csnk2a1 gene product) in complex with the bivalent inhibitor KN2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6TEI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | reservoir composition: 30 % (w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5; crystallization drop composition before equilibration: 0.01 ml reservoir solution plus 0.02 ml enzyme stock solution (6 mg/ml enzyme, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5); the bivalent inhibitor KN2 was introduced by extensive soaking |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.19 | 61.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.591 | α = 90 |
b = 127.591 | β = 90 |
c = 124.52 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 PILATUS 6M | 2019-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.920200 | PETRA III, EMBL c/o DESY | P13 (MX1) |
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 | 1.763 | 89.115 | 74 | 0.111 | 0.111 | 0.113 | 0.022 | 0.998 | 20.4 | 26.5 | 74986 | 29.81 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.763 | 1.921 | 16.4 | 2.229 | 2.229 | 2.27 | 0.428 | 0.697 | 27.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 6TEI | 1.77 | 73.06 | 1.33 | 74959 | 1476 | 74.91 | 0.1743 | 0.1739 | 0.1947 | 40.29 |
Temperature Factor Modeling | ||||||
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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 | 21.6825 |
f_angle_d | 0.7129 |
f_chiral_restr | 0.05 |
f_bond_d | 0.0047 |
f_plane_restr | 0.0045 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5597 |
Nucleic Acid Atoms | |
Solvent Atoms | 419 |
Heterogen Atoms | 124 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHENIX | phasing |
PHENIX | refinement |