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Crystal structure of human IgE (2F10) in complex with Der p 2.0103
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KTJ 1KTJ, 6OY4 experimental model PDB 6OY4 1KTJ, 6OY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 Index A1, Salt: None; Buffer: 0.1M Citric acid pH 3.5; Precipitant: 2.0M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.776 α = 90 b = 231.458 β = 94.338 c = 51.791 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 XE 16M 2020-05-29 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 2.097 40 96.6 0.097 0.097 0.113 0.058 0.987 16.9 3.6 68319
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 2.1 2.14 86.3 0.428 0.428 0.509 0.269 0.824 1.9 3.1
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 1KTJ, 6OY4 2.1 38.606 68207 3560 96.362 0.212 0.2104 0.2167 0.2466 0.2492 42.213
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] -0.086 -1.146 -0.582 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_dihedral_angle_3_deg 12.834 r_dihedral_angle_4_deg 11.995 r_dihedral_angle_1_deg 6.009 r_lrange_it 5.94 r_lrange_other 5.861 r_scangle_it 3.133 r_scangle_other 2.93 r_mcangle_it 2.464 r_mcangle_other 2.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_dihedral_angle_3_deg 12.834 r_dihedral_angle_4_deg 11.995 r_dihedral_angle_1_deg 6.009 r_lrange_it 5.94 r_lrange_other 5.861 r_scangle_it 3.133 r_scangle_other 2.93 r_mcangle_it 2.464 r_mcangle_other 2.464 r_angle_other_deg 2.37 r_scbond_it 2.008 r_scbond_other 1.804 r_angle_refined_deg 1.54 r_mcbond_it 1.513 r_mcbond_other 1.512 r_nbd_other 0.302 r_symmetry_xyhbond_nbd_refined 0.271 r_symmetry_nbd_other 0.223 r_symmetry_nbd_refined 0.196 r_nbd_refined 0.184 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.153 r_ncsr_local_group_3 0.123 r_ncsr_local_group_1 0.119 r_ncsr_local_group_2 0.105 r_chiral_restr 0.094 r_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.036 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8267 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing