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Crystal structure the extracellular region of the epidermal growth factor receptor variant III (EGFRvIII) at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YY9 amino acids 310-500 and 501-614
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 7mg/ml protein, 27.5% PEG 3350, 5% glycerol, 100 mM HEPES, pH 7.0, +5% glycerol for cryo
Crystal Properties Matthews coefficient Solvent content 3.11 60.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.579 α = 90 b = 97.127 β = 90 c = 115.323 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 MAR CCD 300 mm 2009-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0722 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.3 49.58 98.2 0.073 0.084 0.041 0.999 10.9 4 7669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.48 97.1 0.733 0.841 0.403 0.85 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.301 49.58 7646 384 97.6 0.2878 0.2861 0.288 0.3197 0.3264 RANDOM 147.84
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] -34.6208 -32.0747 66.6955
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.82 t_omega_torsion 2.5 t_angle_deg 1.02 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.82 t_omega_torsion 2.5 t_angle_deg 1.02 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2278 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing