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The crystal structure of the murine class IA PI 3-kinase p110delta in complex with GDC-0941.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RD0 PDB ENTRY 2RD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 20% (V/V) GLYCEROL, 10% (W/V) PEG 4K, 30 MM NANO3, 30 MM NA2HPO4, 30 MM (NH4)2SO4, 100 MM IMIDAZOLE PH 6.8
Crystal Properties Matthews coefficient Solvent content 2.44 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.72 α = 90 b = 64.04 β = 103.62 c = 117.74 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 CCD 2008-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 66.67 99.6 0.07 11.47 3.54 45958 -3.7 48.641
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.32 100 0.62 1.76 3.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2RD0 2.3 58.12 44533 1422 99.5 0.22175 0.21991 0.2255 0.27926 0.2854 RANDOM 23.471
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] -0.17 -0.21 1.64 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.752 r_dihedral_angle_4_deg 22.402 r_dihedral_angle_3_deg 17.961 r_dihedral_angle_1_deg 5.818 r_scangle_it 3.103 r_scbond_it 2.046 r_angle_refined_deg 1.44 r_mcangle_it 1.184 r_mcbond_it 0.637 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.752 r_dihedral_angle_4_deg 22.402 r_dihedral_angle_3_deg 17.961 r_dihedral_angle_1_deg 5.818 r_scangle_it 3.103 r_scbond_it 2.046 r_angle_refined_deg 1.44 r_mcangle_it 1.184 r_mcbond_it 0.637 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6633 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing