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Closed structure of active SHP2 mutant E76K bound to SHP099 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291 100 mM bicine pH 9, 100 mM NaCl, 19 % PEG MME 550
Crystal Properties Matthews coefficient Solvent content 2.11 37.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.715 α = 90 b = 54.141 β = 90 c = 218.847 γ = 90
Symmetry Space Group P 2 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 315r 2016-05-01 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2016-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9795 ALS 8.2.2 2 SYNCHROTRON SSRL BEAMLINE BL14-1 1.1270 SSRL BL14-1
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 2.68 72.95 99.3 0.981 6.2 13.4 14269 42.9596256648
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 2.68 2.83 94.9 0.874 2.6 13.8
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 4DGP 2.68 54.71 1.33 14212 1420 99.23 0.2107 0.2046 0.2049 0.2651 0.2655 56.2
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 17.1003335969 f_angle_d 0.511424802676 f_chiral_restr 0.082522582629 f_plane_restr 0.00224959665637 f_bond_d 0.00204849580637
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3989 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 23
Software Software Software Name Purpose Blu-Ice data collection MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building PHENIX refinement