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Crystal structure of HPK1 (MAP4K1) complex with inhibitor A-745
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 296 20% PEG1000, 100 mM Li2SO4, 100 mM Sodium Citrate, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.81 56.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.37 α = 90 b = 69.37 β = 90 c = 323.59 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS 6M 2017-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.786 80.9 98.9 0.029 17.6 11 75564 26.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.787 1.817 0.405
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3ggf 1.786 80.9 75564 3744 98.8 0.1867 0.1857 0.1832 0.2054 0.2071 RANDOM 29.2
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] -1.7366 -1.7366 3.4732
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.04 t_omega_torsion 3.3 t_angle_deg 0.88 t_bond_d 0.008 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 15.04 t_omega_torsion 3.3 t_angle_deg 0.88 t_bond_d 0.008 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 4541 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 67
Software Software Software Name Purpose XDS data reduction XSCALE data scaling BUSTER refinement PDB_EXTRACT data extraction