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CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH COENZYME-A 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 75mM MES, pH 6; 16%w/v PEG 4000; 125mM ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.4 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.646 α = 90 b = 106.664 β = 90 c = 114.512 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 1.7 48.9 95.1 0.126 0.046 0.995 9.9 8.13 80675 21.4
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 1.7 1.73 94.9 1.005 0.37 0.811 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 NONE 5OMO 1.7 48.9 80615 4190 94.77 0.191 0.189 0.1899 0.2332 0.2347 25.328
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] 0.748 0.844 -1.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.574 r_dihedral_angle_4_deg 17.748 r_dihedral_angle_3_deg 14.353 r_lrange_it 6.591 r_dihedral_angle_1_deg 5.878 r_scangle_it 4.335 r_scbond_it 2.922 r_mcangle_it 2.586 r_mcbond_it 1.861 r_angle_refined_deg 1.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.574 r_dihedral_angle_4_deg 17.748 r_dihedral_angle_3_deg 14.353 r_lrange_it 6.591 r_dihedral_angle_1_deg 5.878 r_scangle_it 4.335 r_scbond_it 2.922 r_mcangle_it 2.586 r_mcbond_it 1.861 r_angle_refined_deg 1.612 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.181 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.118 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5503 Nucleic Acid Atoms Solvent Atoms 667 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing