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CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 COMPLEXED WITH 3R-HYDROXY-4E-DECENOYL-CoA AND REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 100 mM MES, pH 6, 17 % w/v Polyethylene glycol 4000, 150 mM Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.9 57.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.285 α = 90 b = 126.869 β = 90 c = 225.342 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 EIGER X 16M Kirkpatrick-Baez mirror pair 2023-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.92 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.29 49.275 99.8 0.089 0.999 19.9 13.4 84773 54.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.33 1.5 0.621 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 2.44 49.275 70610 3539 99.943 0.175 0.1736 0.1831 0.2068 0.2149 71.548
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] -5.077 3.257 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.965 r_dihedral_angle_3_deg 13.479 r_lrange_it 7.317 r_lrange_other 7.31 r_dihedral_angle_2_deg 7.214 r_dihedral_angle_1_deg 5.953 r_scangle_it 5.722 r_scangle_other 5.662 r_scbond_it 3.8 r_scbond_other 3.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.965 r_dihedral_angle_3_deg 13.479 r_lrange_it 7.317 r_lrange_other 7.31 r_dihedral_angle_2_deg 7.214 r_dihedral_angle_1_deg 5.953 r_scangle_it 5.722 r_scangle_other 5.662 r_scbond_it 3.8 r_scbond_other 3.751 r_mcangle_it 3.721 r_mcangle_other 3.721 r_mcbond_it 2.552 r_mcbond_other 2.552 r_chiral_restr_other 2.141 r_angle_refined_deg 1.435 r_dihedral_angle_other_2_deg 1.418 r_angle_other_deg 0.669 r_nbd_other 0.238 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.132 r_ncsr_local_group_1 0.086 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10979 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 223
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing