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Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) in complex with a covalent inhibitor N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-methyl-9H-purin-2-yl}pyrrolidin-3-yl]propanamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 Salt: 0.2 M Ammonium sulfate
Precipitant: 19.5 %w/v PEG 8000
Buffer: 0.1 M HEPES (pH 7.50)
Precipitant: 10.0 %v/v iso-propanol
Crystal Properties Matthews coefficient Solvent content 1.8 31.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.722 α = 90 b = 69.62 β = 90 c = 112.029 γ = 90
Symmetry Space Group P 21 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 98 CCD RAYONIX MX-300 2014-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1 CLSI 08ID-1
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 1.58 43.64 100 0.076 20.4 5.94 37945 25.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.64 100 0.965 1.97 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.58 43.64 37878 1863 99.4 0.201 0.199 0.1986 0.223 0.2213 RANDOM 30.5
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] 1.53 0.16 -1.69
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 2.72 c_scbond_it 1.93 c_mcangle_it 1.92 c_mcbond_it 1.23 c_angle_deg 0.8 c_improper_angle_d 0.62 c_bond_d 0.004 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 2.72 c_scbond_it 1.93 c_mcangle_it 1.92 c_mcbond_it 1.23 c_angle_deg 0.8 c_improper_angle_d 0.62 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2321 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 32
Software Software Software Name Purpose CNX refinement SCALEPACK data scaling CNX phasing autoPROC data scaling