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Crystal Structure of the Drosophila Epidermal Growth Factor Receptor ectodomain in complex with Spitz
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I2T dEGFR domains I-IV (pdb entry 3I2T)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 294 1.5 M sodium potassium phosphate, pH 6.9
4% tert-butanol
, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 4.58 73.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.208 α = 90 b = 124.239 β = 90 c = 186.508 γ = 90
Symmetry Space Group P 21 21 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 270 Rh coated Si monochromatic mirrors 2007-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91790 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 3.14 40.5 99.8 0.147 10.8 6.1 47481 45880 2 2 68.6
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) 3.2 3.34 100 0.567 2 6.2 4714
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 dEGFR domains I-IV (pdb entry 3I2T) 3.2 40 2 2 45880 41290 4589 99.79 0.2405 0.2405 0.23664 0.2383 0.27542 0.2769 RANDOM 80.197
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] -0.3 0.38 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.155 r_dihedral_angle_3_deg 17.073 r_dihedral_angle_4_deg 15.641 r_dihedral_angle_1_deg 5.464 r_scangle_it 1.374 r_angle_refined_deg 1.126 r_scbond_it 0.74 r_mcangle_it 0.608 r_mcbond_it 0.314 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.155 r_dihedral_angle_3_deg 17.073 r_dihedral_angle_4_deg 15.641 r_dihedral_angle_1_deg 5.464 r_scangle_it 1.374 r_angle_refined_deg 1.126 r_scbond_it 0.74 r_mcangle_it 0.608 r_mcbond_it 0.314 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9014 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 199
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling