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X-ray structure of apo human soluble Epoxide Hydrolase C-terminal Domain (hsEH CTD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ANS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277.15 22.5% PEG 3350, 0.2 M malic acid
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.224 α = 90 b = 80.139 β = 95.39 c = 104.696 γ = 90
Symmetry Space Group I 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 PILATUS 6M-F 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.6 70.51 99.9 0.21 0.235 5.7 5.077 114202 22492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.60012 29.6003 0.741 0.831
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 (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 3ANS 2.6 70.51 21388 1101 99.9 0.24755 0.24599 0.2467 0.27704 0.2759 RANDOM 45.454
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] -4.08 1.11 -3.2 6.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.732 r_dihedral_angle_3_deg 15.291 r_dihedral_angle_4_deg 13.764 r_long_range_B_refined 8.989 r_long_range_B_other 8.989 r_dihedral_angle_1_deg 5.804 r_scangle_other 4.708 r_mcangle_it 4.618 r_mcangle_other 4.618 r_scbond_it 2.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.732 r_dihedral_angle_3_deg 15.291 r_dihedral_angle_4_deg 13.764 r_long_range_B_refined 8.989 r_long_range_B_other 8.989 r_dihedral_angle_1_deg 5.804 r_scangle_other 4.708 r_mcangle_it 4.618 r_mcangle_other 4.618 r_scbond_it 2.789 r_scbond_other 2.785 r_mcbond_it 2.784 r_mcbond_other 2.778 r_angle_refined_deg 1.449 r_angle_other_deg 1.001 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5086 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing