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Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IHY PDB ENTRY 3IHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% PEG3350, 0.2M ammonium acetate, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.686 α = 90 b = 141.151 β = 90 c = 163.975 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 CCD ADSC QUANTUM 315 mirrors 2009-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97890 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.25 70.9 99.3 0.092 0.092 12.4 4.8 68403 68403 31.439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.37 95.8 0.451 0.451 1.5 2.8 9539
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3IHY 2.25 70.9 64837 64837 3491 99.26 0.21078 0.20862 0.2038 0.2507 0.2419 RANDOM 29.677
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] -1.91 -0.63 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.536 r_dihedral_angle_4_deg 20.025 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 4.885 r_scangle_it 2.046 r_scbond_it 1.251 r_angle_refined_deg 1.068 r_angle_other_deg 0.853 r_mcangle_it 0.737 r_mcbond_it 0.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.536 r_dihedral_angle_4_deg 20.025 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 4.885 r_scangle_it 2.046 r_scbond_it 1.251 r_angle_refined_deg 1.068 r_angle_other_deg 0.853 r_mcangle_it 0.737 r_mcbond_it 0.376 r_mcbond_other 0.076 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8713 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 54
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling