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STX-478, a Mutant-Selective, Allosteric Inhibitor bound to PI3Kalpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.1 M MES pH 6.8, 500mM NaCl, 8% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.79 55.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.34 α = 90 b = 124.72 β = 92.8 c = 165.84 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU JUPITER 210 2022-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.11 48.77 100 0.088 0.095 0.036 0.999 14.4 6.9 63223
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.11 3.19 99.9 0.841 0.908 0.34 0.786 7.1
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 3.11 48.77 60150 3067 99.95 0.21098 0.20812 0.2103 0.26653 0.2644 RANDOM 106.05
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] 4.54 0.33 -1.95 -2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.963 r_long_range_B_refined 13.206 r_long_range_B_other 13.206 r_mcangle_other 9.367 r_mcangle_it 9.366 r_scangle_other 9.247 r_dihedral_angle_1_deg 6.654 r_mcbond_it 5.883 r_mcbond_other 5.879 r_scbond_it 5.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.963 r_long_range_B_refined 13.206 r_long_range_B_other 13.206 r_mcangle_other 9.367 r_mcangle_it 9.366 r_scangle_other 9.247 r_dihedral_angle_1_deg 6.654 r_mcbond_it 5.883 r_mcbond_other 5.879 r_scbond_it 5.528 r_scbond_other 5.527 r_dihedral_angle_2_deg 5.422 r_angle_refined_deg 0.97 r_angle_other_deg 0.345 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20529 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement Aimless data scaling REFMAC phasing XDS data reduction