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nSH2 domain of p85-alpha subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IUI PDB entry 2IUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.05 M cadmium sulfate hydrate, 0.1 M HEPES, pH 7.5, 1.0 M sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 1.75 29.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.795 α = 90 b = 46.536 β = 90 c = 50.089 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 PIXEL RIGAKU HyPix-6000HE 2019-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.14 26.9 97.6 0.981 13.8 4.4 37579 7.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.18 0.512
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 2IUI 1.14 26.9 1.34 37548 1868 97.46 0.1341 0.1334 0.1346 0.147 0.1481 11.69
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 26.3692 f_angle_d 1.2138 f_chiral_restr 0.0831 f_bond_d 0.0092 f_plane_restr 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 973 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling PHENIX phasing