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Crystal structure of EGFR T790M/C797S/L858R mutant in complex with (2-((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)-5-nitrophenyl)amino)pyrimidin-4-yl)amino)phenyl)dimethylphosphine oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 1M sodium citrate, 0.1M CHES ph 9.0
Crystal Properties Matthews coefficient Solvent content 3.49 64.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.44 α = 90 b = 145.44 β = 90 c = 145.44 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 80 PIXEL DECTRIS PILATUS 6M 2025-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97861 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.84 34.281 98.9 0.088 0.998 11.1 15.4 12099 73.92
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 2.84 6.1135 0.998
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.84 34.28 1.33 12099 1215 98.9 0.2348 0.2281 0.2282 0.2939 0.2938 69.22
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 22.1493 f_angle_d 1.2712 f_chiral_restr 0.0609 f_bond_d 0.0113 f_plane_restr 0.0099
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2435 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 37
Software Software Software Name Purpose PHENIX model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing