☰ Navigation Tabs
Soluble epoxide hydrolase in complex with PROTAC FL412
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 293 20% w/v PEG 3350, 0.2M Ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.01 38.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.125 α = 90 b = 80.182 β = 91.54 c = 89.417 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 1.42 47.15 99.3 0.071 0.085 0.046 0.996 9.4 3.4 124511
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 1.42 1.44 97.6 0.989 1.177 0.63 0.592 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.42 47.15 118003 6472 99.21 0.18904 0.18733 0.21972 0.2403 RANDOM 21.737
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] 0.65 -0.55 -1.28 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.155 r_dihedral_angle_3_deg 12.539 r_dihedral_angle_1_deg 7.108 r_long_range_B_refined 6.007 r_long_range_B_other 6.007 r_scangle_other 4.207 r_mcangle_it 3.094 r_mcangle_other 3.094 r_scbond_it 2.755 r_scbond_other 2.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.155 r_dihedral_angle_3_deg 12.539 r_dihedral_angle_1_deg 7.108 r_long_range_B_refined 6.007 r_long_range_B_other 6.007 r_scangle_other 4.207 r_mcangle_it 3.094 r_mcangle_other 3.094 r_scbond_it 2.755 r_scbond_other 2.755 r_mcbond_it 2.131 r_mcbond_other 2.127 r_angle_refined_deg 1.834 r_angle_other_deg 0.622 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 5088 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction