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Structure of the extracellular domain of human epidermal growth factor (EGF) receptor in an inactive (low pH) complex with EGF.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6B PDB ENTRY 1M6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 297 PEG3400,ammonium sulfate, magnesium sulfate, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.62 66.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.17 α = 90 b = 103.66 β = 119.27 c = 101.49 γ = 90
Symmetry Space Group C 1 2 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 4 2000-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.94 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 98 0.048 12 3.5 26060 26060 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 50 95.4 0.34 2.2 2.9 3252
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1M6B 2.8 20 1 23435 23435 2563 100 0.2474 0.24747 0.24074 0.30985 RANDOM 14.786
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] -1.67 -0.74 -3.92 4.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.206 r_scangle_it 4.139 r_scbond_it 2.319 r_angle_refined_deg 1.766 r_mcangle_it 1.206 r_mcbond_it 0.608 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.237 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.206 r_scangle_it 4.139 r_scbond_it 2.319 r_angle_refined_deg 1.766 r_mcangle_it 1.206 r_mcbond_it 0.608 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.237 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4974 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing