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HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 9
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 volume: 30.0 uL
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: 17.0 %w/v (7.1830985915 uL of stock 71.0 %w/v) 1,6 hexanediol
Additive: 0.02 M (6.0 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
15mg/ml
Crystal Properties Matthews coefficient Solvent content 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.19 α = 67.33 b = 84.26 β = 73.51 c = 87.32 γ = 76.15
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 PILATUS3 6M 2018-04-18 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 1.85 78.71 88.1 0.995 9.9 3.5 67438
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 1.85 2.13 0.54
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 1.85 78.71 67437 3427 54.1 0.198 0.195 0.1963 0.248 0.2473 RANDOM 45.35
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] -1.1051 0.5332 0.06 1.4811 -0.3408 -0.3761
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.94 t_omega_torsion 2.95 t_angle_deg 1.08 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 19.94 t_omega_torsion 2.95 t_angle_deg 1.08 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 8995 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 137
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling BUSTER phasing