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Crystal structure of EGFR_DMX in complex with compound 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Crystal Properties Matthews coefficient Solvent content 3.36 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.687 α = 90 b = 144.687 β = 90 c = 144.687 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 9M 2018-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
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 2.06 45.75 99.5 0.057 0.059 0.016 1 22.7 13.8 30952
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 2.06 2.12 98.3 1.458 1.515 0.409 0.72 13.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5EDQ 2.2 20 24229 1310 99.37 0.18778 0.18577 0.22445 0.2373 RANDOM 57.309
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 35.283 r_dihedral_angle_3_deg 18.766 r_dihedral_angle_4_deg 16.979 r_long_range_B_refined 13.178 r_long_range_B_other 13.178 r_scangle_other 9.18 r_mcangle_it 8.478 r_mcangle_other 8.476 r_scbond_it 6.61 r_scbond_other 6.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.283 r_dihedral_angle_3_deg 18.766 r_dihedral_angle_4_deg 16.979 r_long_range_B_refined 13.178 r_long_range_B_other 13.178 r_scangle_other 9.18 r_mcangle_it 8.478 r_mcangle_other 8.476 r_scbond_it 6.61 r_scbond_other 6.608 r_mcbond_other 6.187 r_mcbond_it 6.183 r_dihedral_angle_1_deg 5.656 r_angle_refined_deg 1.574 r_angle_other_deg 1.373 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 2394 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing