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Crystal structure of EGFR complexed with N-[4-[4-amino-6-ethynyl-5-(3-quinolyl)pyrrolo[2,3-d]pyrimidin-7-yl]norbornan-1-yl]pyrimidine-5-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Analysis by outsourcing.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 1.2 M K/Na-tartrate, 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.52 65.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.92 α = 90 b = 146.92 β = 90 c = 146.92 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 EIGER X 16M 2020-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99981 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.32 103.89 100 1 21.8 24.7 22851
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 2.32 2.37 100 0.607
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 Analysis by outsourcing. 2.32 103.89 21538 1296 100 0.18863 0.18565 0.191 0.23801 0.2406 RANDOM 79.282
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 37.668 r_long_range_B_other 21.106 r_long_range_B_refined 21.104 r_scangle_other 18.562 r_mcangle_other 16.486 r_mcangle_it 16.483 r_scbond_it 14.223 r_scbond_other 14.217 r_dihedral_angle_4_deg 13.699 r_dihedral_angle_3_deg 13.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.668 r_long_range_B_other 21.106 r_long_range_B_refined 21.104 r_scangle_other 18.562 r_mcangle_other 16.486 r_mcangle_it 16.483 r_scbond_it 14.223 r_scbond_other 14.217 r_dihedral_angle_4_deg 13.699 r_dihedral_angle_3_deg 13.106 r_mcbond_it 12.919 r_mcbond_other 12.907 r_dihedral_angle_1_deg 6.665 r_angle_refined_deg 1.584 r_angle_other_deg 1.242 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2504 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 39
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement