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Crystal structure of PI3Ka H1047R mutant in complex with PRT7140 in allosteric pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1M MES pH6.50-6.80, 500mM Sodium chloride, 7-9% PEG3350
Crystal Properties Matthews coefficient Solvent content 5.8 78.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.99 α = 90 b = 125.78 β = 91.5 c = 167.45 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 PIXEL DECTRIS EIGER X 16M 2023-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03322 PETRA III, DESY P11
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 3.61 48.83 99.2 0.087 0.102 0.053 0.999 13.5 7.2 40827
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 3.61 3.76 99.8 0.819 0.957 0.491 0.833 2.5
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 3.61 48.83 38875 1949 99.04 0.24238 0.23959 0.3486 0.29529 0.3795 RANDOM 167.897
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] -0.86 -4.28 -7.34 8.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.42 r_long_range_B_refined 20.423 r_long_range_B_other 20.423 r_dihedral_angle_4_deg 16.661 r_dihedral_angle_3_deg 16.419 r_mcangle_it 12.752 r_mcangle_other 12.752 r_scangle_other 11.328 r_mcbond_it 7.67 r_mcbond_other 7.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.42 r_long_range_B_refined 20.423 r_long_range_B_other 20.423 r_dihedral_angle_4_deg 16.661 r_dihedral_angle_3_deg 16.419 r_mcangle_it 12.752 r_mcangle_other 12.752 r_scangle_other 11.328 r_mcbond_it 7.67 r_mcbond_other 7.669 r_dihedral_angle_1_deg 7.299 r_scbond_it 6.439 r_scbond_other 6.439 r_angle_refined_deg 1.538 r_angle_other_deg 1.225 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.002 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 10448 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing