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HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286.15 Well Ingredients:
Buffer: 0.1 M (3.0 uL of stock 1.0 M) Tris (pH 8.00)
Salt: 0.01 M (0.6 uL of stock 0.5 M) Magnesium sulfate hydrate
Precipitant: 22.0 %w/v (9.2957746479 uL of stock 71.0 %w/v) 1,6 hexanediol
Additive: 0.04 M (12.0 uL of stock 0.1 M) Barium Acetate
Plate setup temperature: 13 C
Plate incubation temperature: 13 C
Drop volume from well: 0.3 uL
Drop protein volume: 0.2 uL
Protein concentration 15mg/ml
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.94 α = 87.22 b = 57.97 β = 86.09 c = 62.13 γ = 66.51
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 6M 2018-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.53 61.97 82 0.998 13.4 3.4 73864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.63 0.891
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 1.59 61.97 72308 3858 81.5 0.191 0.189 0.1933 0.221 0.1986 RANDOM 29.13
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] -3.8389 0.1592 5.0949 3.0627 -0.2807 0.7762
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.89 t_omega_torsion 3.24 t_angle_deg 0.99 t_bond_d 0.01 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 17.89 t_omega_torsion 3.24 t_angle_deg 0.99 t_bond_d 0.01 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 4560 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 60
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling BUSTER phasing