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Crystal structure of the kinase domain of EGFR exon-19 (del-747-749) mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289.15 28% PEG 400, 0.1 M Na Hepes pH 7.5, 0.2 M Calcium Chloride
Crystal Properties Matthews coefficient Solvent content 3.64 66.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.42 α = 90 b = 149.42 β = 90 c = 149.42 γ = 90
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 DECTRIS EIGER X 16M undulator 2019-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.96 105.66 100 0.259 0.263 0.044 0.999 15.4 36.1 11749
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.96 3.14 100 6.596 6.69 1.11 0.438 36.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1M17 2.96 74.71 1.34 11715 561 99.72 0.2422 0.2403 0.2774 0.2617 104.92
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 5.2813 f_angle_d 0.7663 f_chiral_restr 0.0466 f_plane_restr 0.0052 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2338 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction SCALA data scaling PHASER phasing