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The crystal structure of the murine class IA PI 3-kinase p110delta in complex with INK654.
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 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.882 α = 90 b = 64.791 β = 103.21 c = 117.713 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 2008-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.6 69.67 99.2 0.09 19.45 5.22 32463 -3.7 54.589
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 2.6 2.62 96.9 0.29 6.77 5.34
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 2.6 66.52 31443 1018 99.23 0.21177 0.21008 0.213 0.26429 0.2673 RANDOM 12.437
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] -3.19 1.05 3.23 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.241 r_dihedral_angle_4_deg 20.161 r_dihedral_angle_3_deg 17.969 r_dihedral_angle_1_deg 5.673 r_scangle_it 2.452 r_scbond_it 1.519 r_angle_refined_deg 1.306 r_mcangle_it 0.899 r_mcbond_it 0.462 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.241 r_dihedral_angle_4_deg 20.161 r_dihedral_angle_3_deg 17.969 r_dihedral_angle_1_deg 5.673 r_scangle_it 2.452 r_scbond_it 1.519 r_angle_refined_deg 1.306 r_mcangle_it 0.899 r_mcbond_it 0.462 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.091 r_bond_refined_d 0.011 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 49 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing