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Crystal Structure of wild-type EGFR in complex with the reversible inhibitor Sevabertinib (BAY 2927088)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 285 HEPES, sodium succinate
Crystal Properties Matthews coefficient Solvent content 3.37 63.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.43 α = 90 b = 147.43 β = 90 c = 147.43 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 PILATUS 6M-F 2019-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 PETRA III, DESY P11
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 2.14 30 100 0.133 0.14 0.041 0.994 12.1 11.4 29387
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 2.14 2.26 100 0.709 0.743 0.22 0.855 11.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.142 28.93 29377 1224 99.932 0.158 0.1561 0.1647 0.2102 0.218 57.7
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 34.954 r_dihedral_angle_4_deg 16.718 r_dihedral_angle_3_deg 16.28 r_lrange_it 11.667 r_lrange_other 11.626 r_dihedral_angle_1_deg 7.013 r_scangle_it 5.132 r_scangle_other 5.13 r_mcangle_it 4.439 r_mcangle_other 4.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.954 r_dihedral_angle_4_deg 16.718 r_dihedral_angle_3_deg 16.28 r_lrange_it 11.667 r_lrange_other 11.626 r_dihedral_angle_1_deg 7.013 r_scangle_it 5.132 r_scangle_other 5.13 r_mcangle_it 4.439 r_mcangle_other 4.438 r_scbond_it 3.374 r_scbond_other 3.373 r_mcbond_it 2.862 r_mcbond_other 2.861 r_angle_refined_deg 1.38 r_angle_other_deg 1.187 r_xyhbond_nbd_refined 0.265 r_symmetry_xyhbond_nbd_refined 0.232 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.188 r_nbd_other 0.181 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_other 0.082 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2592 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction PHASER phasing