6NG0
Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with sunitinib in the inactive state.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 286.15 | 200 nl protein (15 mg/ml) plus 300 nl reservoir solution (0.1 M tris, pH 8.0, 17.5 % 1,6-Hexanediol, 10 mM magnesium sulfate, 24 mM Barium acetate) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.81 | α = 82.44 |
b = 58.92 | β = 82.31 |
c = 60.93 | γ = 64.34 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 180 | PIXEL | DECTRIS PILATUS3 6M | 2018-08-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.000 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.026 | 60.176 | 97.3 | 0.036 | 0.999 | 14.9 | 3.6 | 43684 | 44.17 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.026 | 2.061 | 96.1 | 0.501 | 0.872 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.05 | 27.69 | 42208 | 2160 | 97.3 | 0.202 | 0.201 | 0.229 | RANDOM | 57.77 |
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] | |
-8.1079 | -7.9928 | 6.0821 | -0.5908 | -8.1366 | 8.6987 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.71 |
t_omega_torsion | 2.76 |
t_angle_deg | 0.99 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4336 |
Nucleic Acid Atoms | |
Solvent Atoms | 320 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
PHASER | phasing |