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Structure of the extracellular domain of the epidermal growth factor receptor in complex with the Fab fragment of cetuximab/Erbitux/IMC-C225
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NQL PDB ENTRY 1NQL and 1YY8 experimental model PDB 1YY8 PDB ENTRY 1NQL and 1YY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 300 PEG 3450, Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 3.48 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.823 α = 90 b = 70.861 β = 102.48 c = 147.122 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.976 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 50 0.06 0.06 15.9 3.7 47467 47467 0.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 98.8 0.85 0.85 2
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 1NQL and 1YY8 2.605 40 44979 2352 98.21 0.24187 0.23939 0.2911 0.28896 0.3239 RANDOM 33.698
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] 1.54 -1.49 0.81 -3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.684 r_dihedral_angle_4_deg 20.734 r_dihedral_angle_3_deg 19.83 r_dihedral_angle_1_deg 7.724 r_sphericity_free 5.854 r_scangle_it 2.562 r_angle_refined_deg 1.68 r_scbond_it 1.618 r_sphericity_bonded 1.528 r_rigid_bond_restr 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.684 r_dihedral_angle_4_deg 20.734 r_dihedral_angle_3_deg 19.83 r_dihedral_angle_1_deg 7.724 r_sphericity_free 5.854 r_scangle_it 2.562 r_angle_refined_deg 1.68 r_scbond_it 1.618 r_sphericity_bonded 1.528 r_rigid_bond_restr 1.14 r_mcangle_it 1.046 r_mcbond_it 0.625 r_nbtor_refined 0.319 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7910 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 259
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing REFMAC refinement HKL-2000 data reduction