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Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in complex with gefitinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GS2 PDB ENTRY 2GS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 1.1M Sodium citrate, 0.1M MES PH 7.1, 5mg/ml protein, incubated overnight at 4deg with final concentration of 0.5mM gefitinib and 1% DMSO , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.25 62.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.675 α = 90 b = 143.675 β = 90 c = 143.675 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 CCD MARMOSAIC 225 mm CCD 2009-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 45.45 100 0.093 5.7 45.3 17240 -3 51.72
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) 1 2.5 2.64 100 0.449 0.45 1.7 45.7 2503
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2GS2 2.5 45.45 17208 868 100 0.19 0.186 0.1838 0.249 0.247 RANDOM 39.47
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 r_dihedral_angle_2_deg 40.655 r_dihedral_angle_4_deg 20.719 r_dihedral_angle_3_deg 19.233 r_dihedral_angle_1_deg 6.81 r_scangle_it 5.926 r_scbond_it 4.374 r_mcangle_it 2.456 r_angle_refined_deg 2.202 r_mcbond_it 1.792 r_nbtor_refined 0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.655 r_dihedral_angle_4_deg 20.719 r_dihedral_angle_3_deg 19.233 r_dihedral_angle_1_deg 6.81 r_scangle_it 5.926 r_scbond_it 4.374 r_mcangle_it 2.456 r_angle_refined_deg 2.202 r_mcbond_it 1.792 r_nbtor_refined 0.334 r_symmetry_hbond_refined 0.261 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.227 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.127 r_bond_refined_d 0.025 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2338 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 43
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling