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X-ray crystal structure of recombinant Can f 1-C100S in complex with human IgE mAb 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 4.2 277.15 0.2 M NaCl, 0.1 M sodium citrate tribasic dihydrate pH 4.2, 20% w/v PEG 8,000 conditions
Crystal Properties Matthews coefficient Solvent content 2.63 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.407 α = 90 b = 191.156 β = 102.91 c = 88.187 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 EIGER2 S 16M 2023-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979 NSLS-II 17-ID-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 3.12 40 100 0.257 0.278 0.104 0.976 7.47 7 46837
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 3.12 3.17 100 0.749 0.813 0.314 0.598 1.97 6.6
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 (Observed) 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 3.12 39.67 44368 2298 99.94 0.20524 0.20318 0.2126 0.24488 0.253 RANDOM 83.621
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] 1.26 1.71 -2.06 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.904 r_dihedral_angle_2_deg 10.191 r_dihedral_angle_1_deg 6.495 r_long_range_B_refined 5.383 r_long_range_B_other 5.38 r_mcangle_it 2.375 r_mcangle_other 2.375 r_scangle_other 2.251 r_mcbond_it 1.338 r_mcbond_other 1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.904 r_dihedral_angle_2_deg 10.191 r_dihedral_angle_1_deg 6.495 r_long_range_B_refined 5.383 r_long_range_B_other 5.38 r_mcangle_it 2.375 r_mcangle_other 2.375 r_scangle_other 2.251 r_mcbond_it 1.338 r_mcbond_other 1.337 r_angle_refined_deg 1.291 r_scbond_it 1.286 r_scbond_other 1.286 r_angle_other_deg 0.455 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17418 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing