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CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3S-HYDROXYBUTANOYL-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 125mM MES, pH 6; 18%w/v PEG 4000; 175mM ammonium.
Co-crystallized with 2mM CoA.
Crystal Properties Matthews coefficient Solvent content 2.89 57.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.637 α = 90 b = 127.086 β = 90 c = 227.1 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 2.2 65.122 99.6 0.095 0.036 0.998 11.7 7.58 96924 38.6
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 2.2 2.24 100 1.022 0.386 0.715 2.1
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 2.2 65.121 96825 4925 99.476 0.202 0.2003 0.2338 0.2379 55.296
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] -1.626 0.752 0.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.243 r_dihedral_angle_4_deg 19.067 r_dihedral_angle_3_deg 17.262 r_lrange_it 7.31 r_dihedral_angle_1_deg 6.307 r_scangle_it 2.028 r_angle_refined_deg 1.54 r_scbond_it 1.264 r_mcangle_it 1.213 r_mcbond_it 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.243 r_dihedral_angle_4_deg 19.067 r_dihedral_angle_3_deg 17.262 r_lrange_it 7.31 r_dihedral_angle_1_deg 6.307 r_scangle_it 2.028 r_angle_refined_deg 1.54 r_scbond_it 1.264 r_mcangle_it 1.213 r_mcbond_it 0.69 r_nbtor_refined 0.312 r_symmetry_xyhbond_nbd_refined 0.254 r_symmetry_nbd_refined 0.252 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.118 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11036 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 248
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing