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X-Ray Diffraction Crystal Structure of the murine PI3K p110delta in complex with a pan inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 290 26% (V/V) GLYCEROL, 13% (W/V) PEG 4K, 3 MM NANO3, 3 MM NA2HPO4, 3 MM (NH4)2SO4, 100 MM IMIDAZOLE PH 6.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.437 α = 90 b = 143.586 β = 90 c = 220.193 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315r 2012-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9763 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 2.9 45.63 99.8 0.251 0.252 0.266 0.085 11.9 10 22926 40
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 98.8 1.104 1.168 0.377 2.9 9.6 3242
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 2WXH 2.9 45.63 21718 1170 99.74 0.24456 0.24213 0.243 0.29011 0.2877 RANDOM 50.567
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] 2.67 0.02 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.677 r_dihedral_angle_4_deg 19.727 r_dihedral_angle_3_deg 18.737 r_long_range_B_refined 10.834 r_long_range_B_other 10.834 r_dihedral_angle_1_deg 5.662 r_mcangle_it 5.427 r_mcangle_other 5.427 r_scangle_other 4.918 r_mcbond_it 3.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.677 r_dihedral_angle_4_deg 19.727 r_dihedral_angle_3_deg 18.737 r_long_range_B_refined 10.834 r_long_range_B_other 10.834 r_dihedral_angle_1_deg 5.662 r_mcangle_it 5.427 r_mcangle_other 5.427 r_scangle_other 4.918 r_mcbond_it 3.273 r_mcbond_other 3.273 r_scbond_it 2.872 r_scbond_other 2.871 r_angle_refined_deg 1.492 r_angle_other_deg 1.093 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6593 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing