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Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with sunitinib in the inactive state.
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 Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.81 α = 82.44 b = 58.92 β = 82.31 c = 60.93 γ = 64.34
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.2035 0.229 0.2321 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 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
RMS Deviations 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 t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4336 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 58
Software Software Software Name Purpose BUSTER refinement XDS data reduction PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing