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PI3Ka H1047R co-crystal structure with inhibitors in two cryptic pockets (compounds 4 and 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 289 0.4M Sodium Formate, 0.1 M Sodium Citrate, pH 5.2
Crystal Properties Matthews coefficient Solvent content 3.56 65.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 236.94 α = 90 b = 158.48 β = 112.83 c = 121.6 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2022-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 3.35 43.471 99.86 0.095 6.5 6.2 59463 89.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.35 3.37 0.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3.35 43.47 1.34 59463 2937 99.86 0.2112 0.2091 0.2109 0.2513 0.2537 RANDOM 116.69
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.224 f_angle_d 0.6168 f_chiral_restr 0.042 f_plane_restr 0.0035 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20712 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 186
Software Software Software Name Purpose PHENIX refinement