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Crystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in complex with 3S hydroxyhexanoyl-PAN and 3',5', diphosphate adenosine
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 7.5 298 100mM Tris, pH 7.5, 2.1M (NH4)2SO4, 10% octanol
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.833 α = 90 b = 92.997 β = 90 c = 247.469 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 XE CdTe 16M 2024-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7290 MAX IV BioMAX
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 1.7 47.9 100 0.037 0.999 14 13.6 192681
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 1.7 1.73 0.34 1.2
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 1.7 47.9 192522 9602 99.927 0.219 0.217 0.2159 0.2476 0.2436 35.33
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] -0.196 2.677 -2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.179 r_dihedral_angle_4_deg 14.349 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.752 r_lrange_it 5.466 r_scangle_it 3.14 r_mcangle_it 2.152 r_scbond_it 1.893 r_mcbond_it 1.322 r_angle_refined_deg 0.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.179 r_dihedral_angle_4_deg 14.349 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.752 r_lrange_it 5.466 r_scangle_it 3.14 r_mcangle_it 2.152 r_scbond_it 1.893 r_mcbond_it 1.322 r_angle_refined_deg 0.949 r_nbtor_refined 0.303 r_nbd_refined 0.186 r_symmetry_nbd_refined 0.159 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.106 r_chiral_restr 0.073 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11571 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 308
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing