☰ Navigation Tabs
Crystal structure of isolated domain III 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 5 298 12 % PEG 3350, 0.25 M ammonium acetate, 50 mM sodium acetate, pH 5.0, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.34 63.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.373 α = 90 b = 139.122 β = 90.02 c = 175.325 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 2006-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.97950 CHESS F2
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 2.57 50 99.8 0.097 9.7 3.8 231454 231454 1 1 53
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 2.57 2.69 99 0.456 2.4 3.3 22862
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 (All) 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 2.58 43.07 233995 231396 11664 98.89 0.23 0.23 0.227 0.2408 0.291 0.3008 RANDOM 29.071
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] -0.29 -0.04 0.39 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.399 r_dihedral_angle_4_deg 19.334 r_dihedral_angle_3_deg 17.2 r_dihedral_angle_1_deg 6.707 r_scangle_it 1.987 r_angle_refined_deg 1.439 r_scbond_it 1.193 r_mcangle_it 0.757 r_mcbond_it 0.424 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.399 r_dihedral_angle_4_deg 19.334 r_dihedral_angle_3_deg 17.2 r_dihedral_angle_1_deg 6.707 r_scangle_it 1.987 r_angle_refined_deg 1.439 r_scbond_it 1.193 r_mcangle_it 0.757 r_mcbond_it 0.424 r_nbtor_refined 0.303 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_refined 0.145 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37083 Nucleic Acid Atoms Solvent Atoms 1036 Heterogen Atoms 916
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection