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Crystal structure of the catalytically inactive kinase domain of the human epidermal growth factor receptor 3 (HER3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GS7 inactive EGFR kinase domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 5mM AMP-PNP, 2mM MgCl2, 1mM DTT, 1mM TCEP, 0.1M Tris pH8.5, 0.2M lithium sulfate, 25% w/v PEG 3350 supplemented with 0.2% w/v 1,2- Diaminocyclohexane sulfate, 0.2% w/v Diloxanite Furoate, 0.2% w/v Fumaric Acid, 0.2% w/v Spermine, 0.2% w/v Sulfaguanidine, 0.02M Hepes sodium pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.164 α = 90 b = 47.637 β = 108.04 c = 81.281 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 298 CCD ADSC QUANTUM 315r KOHZU: Double Crystal Si(111) 2009-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
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 2.8 50 98.2 0.101 6.9 3.6 17822 17502 1 1 62.94
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) 2.8 2.9 93 0.553 1.7 3.2 1618
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT inactive EGFR kinase domain 2.797 46.463 1.93 17792 17472 894 98.2 0.243 0.241 0.2501 0.283 0.2907 71.101
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] -27.573 0.72 16.173 11.4
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.924 f_angle_d 0.833 f_chiral_restr 0.05 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4533 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection