5OWL
Low salt structure of human protein kinase CK2alpha in complex with 3-aminopropyl-4,5,6,7-tetrabromobenzimidazol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5CQU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 25 % PEG3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS BUFFER, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST THE RESERVOIR SOLUTION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.12 | 60.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.364 | α = 90 |
b = 126.364 | β = 90 |
c = 125.271 | 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 | CCD | ADSC QUANTUM 315r | 2016-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.9660 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 2.23 | 72.75 | 99.75 | 0.09056 | 0.09056 | 12.78 | 6 | 49867 | 52.58 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.23 | 2.31 | 99.8 | 2.437 | 2.437 | 0.426 | 0.81 | 6.1 |
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 | 5cqu | 2.23 | 63.182 | 1.35 | 49832 | 1226 | 99.75 | 0.2114 | 0.2105 | 0.2488 |
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 | 13.256 |
f_angle_d | 0.498 |
f_chiral_restr | 0.043 |
f_plane_restr | 0.003 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5597 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |