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The complex structure of extracellular domain of EGFR and GC1118A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YY9 PDB ENTRY 1YY9
Crystallization Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.389 α = 90 b = 84.172 β = 97.11 c = 97.793 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 95 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 1.9 50 98.1 0.09 19.38 6.9 104241
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 1.87 1.9 84.6 0.94 1.2 5.5
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 1YY9 2.1 19.75 69903 3710 99.69 0.20429 0.20199 0.2084 0.24759 0.2507 RANDOM 46.354
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] 0.04 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.738 r_dihedral_angle_4_deg 16.028 r_dihedral_angle_3_deg 13.903 r_long_range_B_refined 8.506 r_long_range_B_other 8.5 r_scangle_other 7.175 r_dihedral_angle_1_deg 6.634 r_mcangle_it 5.214 r_mcangle_other 5.214 r_scbond_it 4.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.738 r_dihedral_angle_4_deg 16.028 r_dihedral_angle_3_deg 13.903 r_long_range_B_refined 8.506 r_long_range_B_other 8.5 r_scangle_other 7.175 r_dihedral_angle_1_deg 6.634 r_mcangle_it 5.214 r_mcangle_other 5.214 r_scbond_it 4.907 r_scbond_other 4.907 r_mcbond_it 3.903 r_mcbond_other 3.901 r_angle_refined_deg 1.535 r_angle_other_deg 0.83 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 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 7906 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing