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Soluble epoxide hydrolase in complex with PROTAC JSF67
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.05 39.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.395 α = 90 b = 80.362 β = 92.17 c = 90.224 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 16M 2023-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.48 47.41 99.3 0.056 0.067 0.036 0.998 10.3 3.4 111646
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 1.48 1.51 96.3 0.936 1.117 0.602 0.497 3.5
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 1.48 47.41 106133 5464 99.26 0.16778 0.16618 0.1661 0.19918 0.1993 RANDOM 25.515
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] 0.76 -0.83 -1.41 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.779 r_dihedral_angle_2_deg 6.98 r_long_range_B_refined 6.781 r_long_range_B_other 6.78 r_dihedral_angle_1_deg 6.756 r_scangle_other 5.097 r_mcangle_it 3.557 r_mcangle_other 3.557 r_scbond_it 3.477 r_scbond_other 3.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.779 r_dihedral_angle_2_deg 6.98 r_long_range_B_refined 6.781 r_long_range_B_other 6.78 r_dihedral_angle_1_deg 6.756 r_scangle_other 5.097 r_mcangle_it 3.557 r_mcangle_other 3.557 r_scbond_it 3.477 r_scbond_other 3.476 r_mcbond_other 2.528 r_mcbond_it 2.527 r_angle_refined_deg 1.834 r_angle_other_deg 0.639 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 5071 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing