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Idelalisib bound to the p110 subunit of PI3K delta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Crystals for seeding were obtained by vapor diffusion, followed by preparation of diffraction quality crystals.
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.049 α = 90 b = 64.59 β = 103.09 c = 115.96 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 CCD ADSC QUANTUM 315r 2014-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.43 69.18 99.5 0.085 0.053 0.995 9.7 3.6 38471 35.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.53 98.9 0.433 0.273 0.766 2.7 3.4 4009
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2WXF 2.434 69.179 1.34 38469 2000 99.36 0.2171 0.2131 0.2152 0.2888 0.2896 Random selection 40.9772
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 14.806 f_angle_d 1.202 f_chiral_restr 0.044 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6566 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 31
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building