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Crystal structure of 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 3.5 277 0.1 M citric acid pH 3.5; 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.769 α = 90 b = 116.769 β = 90 c = 71.102 γ = 120
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 EIGER2 X 16M 2025-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.729 MAX IV BioMAX
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 2.27 40 99.3 0.144 0.153 0.048 0.987 47.9 11.1 25393
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 2.27 2.31 100 0.911 0.951 0.268 0.834 2.2 12.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.27 27.019 25366 1189 98.831 0.189 0.187 0.1972 0.2435 0.2525 79.42
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] 0.462 0.231 0.462 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.737 r_dihedral_angle_3_deg 10.972 r_dihedral_angle_2_deg 7.285 r_dihedral_angle_1_deg 7.252 r_lrange_it 6.6 r_lrange_other 6.587 r_scangle_it 3.689 r_scangle_other 3.688 r_mcangle_it 3.332 r_mcangle_other 3.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.737 r_dihedral_angle_3_deg 10.972 r_dihedral_angle_2_deg 7.285 r_dihedral_angle_1_deg 7.252 r_lrange_it 6.6 r_lrange_other 6.587 r_scangle_it 3.689 r_scangle_other 3.688 r_mcangle_it 3.332 r_mcangle_other 3.331 r_scbond_it 2.398 r_scbond_other 2.397 r_mcbond_it 2.127 r_mcbond_other 2.127 r_angle_refined_deg 0.991 r_angle_other_deg 0.44 r_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.207 r_nbd_other 0.2 r_nbd_refined 0.191 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_nbd_refined 0.118 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.055 r_bond_other_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3220 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing