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Crystal structure of the HPK1 kinase domain in complex with inhibitor 12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 5 % PEG 8000, 0.01 M propionate-cacodylate-bis-tris (PCTP) pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.56 51.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.536 α = 90 b = 68.011 β = 94.95 c = 63.368 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2022-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.386 63.131 74.8 0.041 0.046 0.02 15.7 5.1 50342 19.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.386 1.486 20 0.845 0.972 0.472 3.9
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 1.386 20.08 50308 2476 74.7 0.2048 0.2033 0.1985 0.2328 0.2256 RANDOM 27.71
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] 0.0537 -0.2632 0.2357 -0.2895
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.48 t_omega_torsion 3.74 t_angle_deg 1.04 t_bond_d 0.011 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.48 t_omega_torsion 3.74 t_angle_deg 1.04 t_bond_d 0.011 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 2253 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 36
Software Software Software Name Purpose BUSTER refinement Aimless data scaling XDS data reduction AMoRE phasing PDB_EXTRACT data extraction