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PI3Ka H1047R co-crystal structure with inhibitor in cryptic pocket (compound 5).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M Sodium Malonate pH 5.0, 10% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.72 54.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.56 α = 90 b = 124.07 β = 93.57 c = 166.47 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 9M 2022-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2 19.99 99.15 0.095 0.98 6.5 19.99 55638
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 3.2 3.31 0.83
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 3.2 19.99 52901 2737 99.19 0.27844 0.27679 0.2754 0.31025 0.3085 RANDOM 86.761
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] 5.26 0.69 0.2 -5.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.596 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_4_deg 13.722 r_dihedral_angle_1_deg 6.738 r_mcangle_it 2.101 r_mcangle_other 2.101 r_scangle_other 1.471 r_angle_refined_deg 1.35 r_angle_other_deg 1.244 r_mcbond_it 1.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.596 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_4_deg 13.722 r_dihedral_angle_1_deg 6.738 r_mcangle_it 2.101 r_mcangle_other 2.101 r_scangle_other 1.471 r_angle_refined_deg 1.35 r_angle_other_deg 1.244 r_mcbond_it 1.146 r_mcbond_other 1.146 r_scbond_it 0.765 r_scbond_other 0.765 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19901 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement