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Human PI3KDELTA in complex with Zandelisib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 283.15 10% PEG 4000, 100 mM KCl, 1 mM TCEP neutral pH, 10 mM CaCl2, 100 mM MES pH 5.8
Crystal Properties Matthews coefficient Solvent content 2.51 51.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.89 α = 90 b = 109.08 β = 90 c = 142.44 γ = 90
Symmetry Space Group P 21 21 21
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 2023-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99999 SLS X10SA
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 2.5 45.45 99.9 0.041 0.045 0.017 1 18.7 6.7 49670
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 2.5 2.58 99.7 1.193 1.296 0.499 0.858 1.6 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6PYR 2.5 45.45 1.35 49577 2399 99.74 0.2327 0.2304 0.2304 0.2776 0.2769 97.2
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 6.8169 f_angle_d 0.5592 f_chiral_restr 0.0385 f_plane_restr 0.0037 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8847 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing