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X-ray crystal structure of recombinant Can f 1 in complex with human IgE 12F3 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Lithium chloride, 20% w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.35 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.528 α = 90 b = 73.95 β = 99.588 c = 77.275 γ = 90
Symmetry Space Group P 1 21 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 9M 2024-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.979 NSLS-II 17-ID-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 1.85 40 98.8 0.106 0.115 0.043 0.997 15.11 7.1 50951
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 1.85 1.88 96.7 0.55 0.596 0.226 0.846 2 6.8
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 1.85 38.127 50932 2465 98.4 0.182 0.1793 0.1874 0.2255 0.2321 23.283
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] -0.16 0.517 1.02 -0.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.192 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_2_deg 9.826 r_dihedral_angle_1_deg 7.089 r_lrange_it 6.799 r_lrange_other 6.7 r_scangle_it 3.116 r_scangle_other 3.116 r_mcangle_it 2.312 r_mcangle_other 2.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.192 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_2_deg 9.826 r_dihedral_angle_1_deg 7.089 r_lrange_it 6.799 r_lrange_other 6.7 r_scangle_it 3.116 r_scangle_other 3.116 r_mcangle_it 2.312 r_mcangle_other 2.312 r_scbond_it 1.979 r_scbond_other 1.978 r_mcbond_it 1.459 r_mcbond_other 1.459 r_angle_refined_deg 1.405 r_angle_other_deg 0.762 r_symmetry_nbd_other 0.22 r_symmetry_xyhbond_nbd_refined 0.208 r_xyhbond_nbd_refined 0.2 r_nbd_other 0.199 r_nbd_refined 0.197 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.128 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4293 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing