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Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 4A80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M HEPES pH 7.5; 0.05 M magnesium chloride hexahydrate; 30% PEG MME 550
Crystal Properties Matthews coefficient Solvent content 2.98 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.928 α = 90 b = 117.535 β = 90 c = 158.622 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 9M 2024-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 2.12 40 99.8 0.087 0.091 0.026 0.998 25.5 12.6 43908
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 2.12 2.16 99.7 0.73 0.764 0.224 0.866 2.1 11.1
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 (All) 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 2.12 39.694 43683 2224 99.783 0.173 0.1708 0.1842 0.2183 0.2254 RANDOM 59.23
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] 1.789 -0.775 -1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.693 r_dihedral_angle_3_deg 11.323 r_lrange_other 9.948 r_lrange_it 9.939 r_dihedral_angle_2_deg 9.879 r_scangle_it 7.222 r_scangle_other 7.221 r_dihedral_angle_1_deg 6.98 r_scbond_it 5.226 r_scbond_other 5.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.693 r_dihedral_angle_3_deg 11.323 r_lrange_other 9.948 r_lrange_it 9.939 r_dihedral_angle_2_deg 9.879 r_scangle_it 7.222 r_scangle_other 7.221 r_dihedral_angle_1_deg 6.98 r_scbond_it 5.226 r_scbond_other 5.225 r_mcangle_it 4.767 r_mcangle_other 4.767 r_mcbond_it 3.677 r_mcbond_other 3.676 r_angle_refined_deg 1.573 r_angle_other_deg 0.822 r_symmetry_nbd_other 0.212 r_nbd_other 0.203 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.174 r_chiral_restr 0.128 r_symmetry_nbd_refined 0.126 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.083 r_bond_other_d 0.011 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4457 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing