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Crystal structure of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YY9 PDB entries 1yy9, 1ce1, and 1dn0 experimental model PDB 1CE1 PDB entries 1yy9, 1ce1, and 1dn0 experimental model PDB 1DN0 PDB entries 1yy9, 1ce1, and 1dn0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 12 % PEG 3350, IM NaCl, 50 mM MES, pH 6.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.09 60.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.743 α = 90 b = 266.242 β = 90 c = 156.381 γ = 90
Symmetry Space Group C 2 2 21
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 2005-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.3 50 100 0.188 5.6 6 21995 21995
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 3.3 3.42 100 0.58 3.1 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 entries 1yy9, 1ce1, and 1dn0 3.3 41.04 21867 20747 1120 99.14 0.286 0.28187 0.2853 0.36715 0.3658 RANDOM 60.921
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] -2.8 10.75 -7.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.473 r_dihedral_angle_3_deg 26.099 r_dihedral_angle_4_deg 21.275 r_dihedral_angle_1_deg 12.202 r_scangle_it 3.456 r_angle_refined_deg 2.647 r_scbond_it 2.025 r_mcangle_it 1.466 r_mcbond_it 0.794 r_symmetry_vdw_refined 0.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.473 r_dihedral_angle_3_deg 26.099 r_dihedral_angle_4_deg 21.275 r_dihedral_angle_1_deg 12.202 r_scangle_it 3.456 r_angle_refined_deg 2.647 r_scbond_it 2.025 r_mcangle_it 1.466 r_mcbond_it 0.794 r_symmetry_vdw_refined 0.372 r_nbd_refined 0.343 r_nbtor_refined 0.343 r_xyhbond_nbd_refined 0.267 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.161 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5524 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 121
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection