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Crystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in complex with 3S-hydroxyhexanoyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 100mM Tris, pH 7.5, 2.1M (NH4)2SO4, 5%v/v octanol
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.08 α = 90 b = 93.692 β = 90 c = 248.677 γ = 90
Symmetry Space Group P 21 21 21
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 X 9M 2024-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96863 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.68 124.7 55.8 0.063 0.989 6.1 4 113963
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.89 0.79 1.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.68 124.7 113963 5600 55.849 0.211 0.2093 0.2092 0.2418 0.2419 29.78
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] -0.107 0.333 -0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.422 r_dihedral_angle_3_deg 13.799 r_dihedral_angle_4_deg 12.124 r_dihedral_angle_1_deg 5.732 r_lrange_it 5.019 r_scangle_it 1.818 r_mcangle_it 1.611 r_scbond_it 1.044 r_mcbond_it 0.896 r_angle_refined_deg 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.422 r_dihedral_angle_3_deg 13.799 r_dihedral_angle_4_deg 12.124 r_dihedral_angle_1_deg 5.732 r_lrange_it 5.019 r_scangle_it 1.818 r_mcangle_it 1.611 r_scbond_it 1.044 r_mcbond_it 0.896 r_angle_refined_deg 0.792 r_nbtor_refined 0.299 r_nbd_refined 0.174 r_symmetry_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.129 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.063 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11651 Nucleic Acid Atoms Solvent Atoms 899 Heterogen Atoms 280
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing