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Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with 3-{4-[(3R,5S)-3-Amino-5-methylpiperidin-1-yl]-6-chloro-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NG0 PDB entry 6NG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286.15 15 mg/mL protein + reservoir (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 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.71 α = 96.43 b = 87.4 β = 99.99 c = 109.071 γ = 108.89
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 PILATUS 6M 2016-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.9 81.34 96.5 0.062 0.04 0.996 10.4 3.5 149381
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 0.547 0.336 0.841 2.3
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 PDB entry 6NG0 1.897 81.34 149378 7448 96.5 0.2162 0.2145 0.206 0.249 0.2408 RANDOM 44.21
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] 4.2878 -6.236 5.1558 2.0776 3.4026 -6.3654
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.4 t_omega_torsion 2.95 t_angle_deg 0.92 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13174 Nucleic Acid Atoms Solvent Atoms 840 Heterogen Atoms 156
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing