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CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH ACETOACETYL-COA AND NADH
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 MES, pH 6; 16%w/v PEG 4000; 150mM ammonium sulfate.
Co-crystallized with 2mM CoA
Crystal Properties Matthews coefficient Solvent content 2.93 57.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.937 α = 90 b = 127.39 β = 90 c = 228.173 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 PILATUS 6M 2018-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972957 ESRF ID23-1
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 2.7 48.88 95.5 0.157 0.06 0.995 11.7 7.77 51199 52.6
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 2.7 2.78 1.092 0.406 0.691 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OMO 2.7 48.88 50871 2540 94.554 0.234 0.2316 0.2733 0.264 72.958
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] 6.068 -1.042 -5.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.071 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 17.798 r_lrange_it 7.179 r_dihedral_angle_1_deg 6.068 r_scangle_it 1.156 r_mcangle_it 1.086 r_angle_refined_deg 1.081 r_scbond_it 0.666 r_mcbond_it 0.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.071 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 17.798 r_lrange_it 7.179 r_dihedral_angle_1_deg 6.068 r_scangle_it 1.156 r_mcangle_it 1.086 r_angle_refined_deg 1.081 r_scbond_it 0.666 r_mcbond_it 0.582 r_nbtor_refined 0.307 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.187 r_xyhbond_nbd_refined 0.13 r_ncsr_local_group_1 0.097 r_chiral_restr 0.095 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11074 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 206
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing