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Crystal structure of rat peroxisomal multifunctional enzyme type-1 complexed with 2E,4E-decadienoyl-CoA, 3R-hydroxy-4E-decenoyl-CoA and NAD
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 6 293 125 mM MES, pH 6; 17 %w/v Polyethylene glycol 4000; 175 mM Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.9 57.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.481 α = 90 b = 126.719 β = 90 c = 226.168 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 Bruker PHOTON II Helios multilayer 2020-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 64.798 99.9 0.291 0.06 0.993 11.6 24 110584 1 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.2 2.4 0.773 0.198 1.1 10.2
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 2.3 64.798 84461 4221 99.844 0.222 0.2205 0.2246 0.2469 0.2486 44.576
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] -0.494 2.322 -1.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.745 r_dihedral_angle_3_deg 13.585 r_dihedral_angle_2_deg 7.61 r_dihedral_angle_1_deg 6.056 r_lrange_it 3.784 r_lrange_other 3.772 r_chiral_restr_other 2.015 r_scangle_it 1.77 r_dihedral_angle_other_2_deg 1.723 r_scangle_other 1.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.745 r_dihedral_angle_3_deg 13.585 r_dihedral_angle_2_deg 7.61 r_dihedral_angle_1_deg 6.056 r_lrange_it 3.784 r_lrange_other 3.772 r_chiral_restr_other 2.015 r_scangle_it 1.77 r_dihedral_angle_other_2_deg 1.723 r_scangle_other 1.703 r_angle_refined_deg 1.457 r_mcangle_it 1.117 r_mcangle_other 1.117 r_scbond_it 1.109 r_scbond_other 1.068 r_angle_other_deg 0.642 r_mcbond_it 0.638 r_mcbond_other 0.638 r_symmetry_nbd_refined 0.238 r_nbd_other 0.219 r_nbd_refined 0.215 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.166 r_xyhbond_nbd_refined 0.153 r_ncsr_local_group_1 0.092 r_symmetry_nbtor_other 0.076 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 10915 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing MOLREP phasing