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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 experimental model PDB 9Y0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.04 M potassium phosphate monobasic; 16% PEG 8000; 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.971 α = 90 b = 70.258 β = 116.375 c = 78.247 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 100 PIXEL DECTRIS EIGER X 4M 2024-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.968 ESRF MASSIF-1
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 2.9 40 91.8 0.1 0.11 0.044 0.988 15.1 5.5 14960
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 2.9 2.95 53.4 0.26 0.322 0.186 0.826 2.2 2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 40 14926 751 90.603 0.199 0.1962 0.257 0.2269 52.908
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] 1.106 1.659 2.415 -3.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.315 r_dihedral_angle_6_deg 8.778 r_lrange_it 6.849 r_lrange_other 6.849 r_dihedral_angle_2_deg 6.464 r_dihedral_angle_1_deg 5.075 r_mcangle_it 3.743 r_mcangle_other 3.743 r_scangle_it 3.47 r_scangle_other 3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.315 r_dihedral_angle_6_deg 8.778 r_lrange_it 6.849 r_lrange_other 6.849 r_dihedral_angle_2_deg 6.464 r_dihedral_angle_1_deg 5.075 r_mcangle_it 3.743 r_mcangle_other 3.743 r_scangle_it 3.47 r_scangle_other 3.47 r_mcbond_it 2.168 r_mcbond_other 2.166 r_scbond_it 2.036 r_scbond_other 2.036 r_angle_refined_deg 1.245 r_angle_other_deg 0.506 r_symmetry_nbd_refined 0.26 r_xyhbond_nbd_refined 0.254 r_symmetry_nbd_other 0.228 r_nbd_other 0.21 r_nbd_refined 0.207 r_nbtor_refined 0.179 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.06 r_chiral_restr 0.055 r_bond_other_d 0.01 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4398 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing