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X-ray crystal structure of human IgE 4C8 Fab complex with Der p 2.0103
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 4 293 1.0 M lithium chloride, 0.3 M citrate, pH 4.0, 25% w/v PEG6000
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.254 α = 90 b = 95.298 β = 105.724 c = 69.209 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 EIGER2 XE 16M 2022-02-22 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 3.05 40 99 0.105 0.105 0.122 0.061 0.984 13.7 3.8 26735
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 3.05 3.1 97.1 0.42 0.42 0.49 0.25 0.82 1.8
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 3.05 39.577 26651 1353 98.532 0.199 0.1967 0.1954 0.2477 0.2403 68.809
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] -1.691 -1.523 6.208 -3.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.338 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_2_deg 8.174 r_lrange_it 7.535 r_lrange_other 7.535 r_dihedral_angle_1_deg 6.291 r_mcangle_it 3.576 r_mcangle_other 3.576 r_scangle_it 3.465 r_scangle_other 3.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.338 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_2_deg 8.174 r_lrange_it 7.535 r_lrange_other 7.535 r_dihedral_angle_1_deg 6.291 r_mcangle_it 3.576 r_mcangle_other 3.576 r_scangle_it 3.465 r_scangle_other 3.465 r_mcbond_it 2.078 r_mcbond_other 2.078 r_scbond_it 2.02 r_scbond_other 2.02 r_angle_refined_deg 1.302 r_angle_other_deg 0.448 r_symmetry_xyhbond_nbd_refined 0.431 r_nbd_other 0.27 r_symmetry_nbd_refined 0.256 r_xyhbond_nbd_refined 0.226 r_symmetry_nbd_other 0.218 r_nbd_refined 0.205 r_nbtor_refined 0.174 r_ncsr_local_group_1 0.144 r_ncsr_local_group_2 0.128 r_ncsr_local_group_3 0.118 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8356 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing