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Soluble epoxide hydrolase in complex with RK3
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 6.5 293 20% PEG5000MME, 0.1M bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.05 39.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.332 α = 90 b = 80.478 β = 92.14 c = 90.038 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 1.49 44.99 99.4 0.041 0.049 0.026 0.999 14.8 3.4 109510
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 1.49 1.51 98.7 0.694 0.825 0.44 0.751 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 1.49 44.09 104114 5370 99.31 0.16457 0.16342 0.18698 0.1981 RANDOM 23.368
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] 0.9 -0.82 -1.32 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.575 r_dihedral_angle_2_deg 7.307 r_dihedral_angle_1_deg 6.877 r_long_range_B_refined 6.547 r_long_range_B_other 6.547 r_scangle_other 5.065 r_mcangle_it 3.662 r_mcangle_other 3.662 r_scbond_it 3.385 r_scbond_other 3.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.575 r_dihedral_angle_2_deg 7.307 r_dihedral_angle_1_deg 6.877 r_long_range_B_refined 6.547 r_long_range_B_other 6.547 r_scangle_other 5.065 r_mcangle_it 3.662 r_mcangle_other 3.662 r_scbond_it 3.385 r_scbond_other 3.384 r_mcbond_it 2.563 r_mcbond_other 2.563 r_angle_refined_deg 1.731 r_angle_other_deg 0.585 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 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 5065 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing MOLREP phasing XDS data reduction