5UNP
Structure of CDC2-Like Kinase 2 (CLK2) in Complex with Compound T-025 [N2-methyl-N4-(pyrimidin-2-ylmethyl)-5-(quinolin-6-yl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine]
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 0.1M Hepes (pH 7.0), 0.2M KBr, 0.2M KSCN, 0.4-1.8% PGA (poly-gama-glutamic acid) and 1-4% PEG MME M.W. 2,000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.58 | 65.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 141.252 | α = 90 |
b = 141.252 | β = 90 |
c = 124.37 | γ = 90 |
Symmetry | |
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Space Group | I 41 |
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 | AREA DETECTOR | ADSC QUANTUM 315r | 2015-05-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | 0.977 | ALS | 5.0.3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.92 | 50 | 99.8 | 23 | 5 | 26725 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | THROUGHOUT | 2.92 | 38.97 | 25181 | 1333 | 99.67 | 0.20229 | 0.20062 | 0.23385 | RANDOM | 106.189 |
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] | |
-2.62 | -2.62 | 5.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.191 |
r_dihedral_angle_4_deg | 18.324 |
r_dihedral_angle_3_deg | 14.975 |
r_dihedral_angle_1_deg | 5.838 |
r_angle_refined_deg | 1.177 |
r_angle_other_deg | 0.734 |
r_chiral_restr | 0.068 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5762 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |