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Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in the apo form
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 COUNTER-DIFFUSION 7.1 293 COUNTER DIFFUSION IN MICROGRAVITY CONDITIONS; COUNTER-DIFFUSION METHOD USING JAXA CRYSTALLISATION BOX (JCB). 40mm X 0.5mm CAPILLARIES WERE FILLED WITH 8.1mg/ml PROTEIN SOLUTION AND INSTALLED INTO JCB SYRINGE CASE FILLED WITH MOTHER LIQUOUR (1.7M Sodium CITRATE, 0.1M MES, 7.1). CRYSTALS WERE IN ORBIT FOR 2.5 MONTHS IN THE PROTEIN CRYSTALLISATION RESEARCH FACILITY ON THE JAPANESE EXPERIMENT MODULE OF THE INTERNATIONAL SPACE STATION., Counter Diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.09 60.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.334 α = 90 b = 141.334 β = 90 c = 141.334 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 RAYONIX MX225HE RHODIUM-COATED MIRRORS (HORIZONTAL AND VERTICAL) 2009-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.75 50 99.9 0.09 6.5 5.1 12348 -3 67.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 100 0.42 1.8 5.1 1782
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 (Observed) 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 2.75 50 12334 617 99.8 0.198 0.196 0.1938 0.243 0.241 RANDOM 52.17
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 40.781 r_dihedral_angle_4_deg 23.454 r_dihedral_angle_3_deg 22.462 r_dihedral_angle_1_deg 6.72 r_scangle_it 4.294 r_scbond_it 2.855 r_mcangle_it 1.824 r_angle_refined_deg 1.821 r_mcbond_it 1.244 r_symmetry_hbond_refined 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.781 r_dihedral_angle_4_deg 23.454 r_dihedral_angle_3_deg 22.462 r_dihedral_angle_1_deg 6.72 r_scangle_it 4.294 r_scbond_it 2.855 r_mcangle_it 1.824 r_angle_refined_deg 1.821 r_mcbond_it 1.244 r_symmetry_hbond_refined 0.346 r_nbtor_refined 0.343 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.269 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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 2301 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling