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X-ray crystal structure of human IgE 4C8 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 0.1 M Tris, 0.1 M sodium formate, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.009 α = 90 b = 80.664 β = 90 c = 164.807 γ = 90
Symmetry Space Group P 21 21 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 EIGER2 XE 16M 2022-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 39.207 99.9 0.158 0.158 0.171 0.064 0.98 16.6 6.9 29122
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.9 0.708 0.708 0.773 0.307 0.819 2 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 7MLH 2.508 39.207 29068 1465 99.818 0.2 0.1978 0.202 0.2471 0.2499 63.554
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] -0.1 -3.385 3.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.465 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 8.549 r_lrange_it 7.924 r_lrange_other 7.917 r_dihedral_angle_1_deg 6.665 r_scangle_it 4.714 r_scangle_other 4.714 r_mcangle_other 4.032 r_mcangle_it 4.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.465 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 8.549 r_lrange_it 7.924 r_lrange_other 7.917 r_dihedral_angle_1_deg 6.665 r_scangle_it 4.714 r_scangle_other 4.714 r_mcangle_other 4.032 r_mcangle_it 4.031 r_scbond_it 2.995 r_scbond_other 2.994 r_mcbond_it 2.547 r_mcbond_other 2.541 r_angle_refined_deg 1.22 r_angle_other_deg 0.417 r_nbd_other 0.307 r_symmetry_nbd_other 0.214 r_xyhbond_nbd_refined 0.214 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.183 r_nbtor_refined 0.172 r_ncsr_local_group_2 0.106 r_ncsr_local_group_1 0.103 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.052 r_symmetry_xyhbond_nbd_other 0.048 r_symmetry_xyhbond_nbd_refined 0.036 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6247 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing