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CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3-KETODECANOYL-COA AND OXIDISED 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 6 295 100mM MES, pH 6; 15%w/v PEG 4000; 150.91mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.8 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.155 α = 90 b = 125.977 β = 90 c = 223.527 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 16M 2020-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.25 62.63 100 0.099 0.042 0.997 8.4 6.45 88285 51.3
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 2.25 2.29 1.388 0.587 0.671 1.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OMO 2.25 62.63 88189 4428 99.931 0.211 0.2093 0.2093 0.2464 0.2464 70
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] -1.711 2.337 -0.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.62 r_dihedral_angle_4_deg 19.46 r_dihedral_angle_3_deg 18.171 r_lrange_it 7.525 r_dihedral_angle_1_deg 6.293 r_scangle_it 2.947 r_mcangle_it 2.085 r_scbond_it 1.794 r_mcbond_it 1.226 r_angle_refined_deg 1.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.62 r_dihedral_angle_4_deg 19.46 r_dihedral_angle_3_deg 18.171 r_lrange_it 7.525 r_dihedral_angle_1_deg 6.293 r_scangle_it 2.947 r_mcangle_it 2.085 r_scbond_it 1.794 r_mcbond_it 1.226 r_angle_refined_deg 1.205 r_nbtor_refined 0.31 r_symmetry_xyhbond_nbd_refined 0.251 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.203 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.1 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11006 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 290
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing