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Crystal structure of nanobody/VHH domain of 34E5 in complex with the extracellular region of the epidermal growth factor variant III (EGFRvIII)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YY9 amino acids 310-500 and 501-614 experimental model PDB 4NC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 70-90 micromolar protein, 15-20% PEG 3350, 100 mM ammonium phosphate, pH 7.4, +20% PEG400 for cryo
Crystal Properties Matthews coefficient Solvent content 3.89 68.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.291 α = 106.92 b = 80.361 β = 103.5 c = 91.841 γ = 104.56
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 RAYONIX MX-300 2015-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 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 2.755 47.31 94.3 0.098 0.114 0.058 0.994 9 3.9 40641
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 2.76 2.87 70 1.954 2.266 1.143 0.333 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2.94 46.55 1.97 34614 1681 98.21 0.2168 0.2149 0.2277 0.2524 0.2574
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.812 f_angle_d 0.869 f_chiral_restr 0.055 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6641 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing