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Crystal Structure of Rat Peroxisomal Multifunctional enzyme Type-1 (RPMFE1) Complexed with Acetoacetyl-CoA and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 295 100 mM MES pH 6.0, 150 mM Ammonium sulphate, 15 % w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.75 55.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.23 α = 90 b = 125.82 β = 90 c = 223.9 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 CCD ADSC QUANTUM 4 2009-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 33.56 83.8 0.13 8 3.8 38432
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 84 0.38 2.4 3.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2X58 2.8 33.56 36256 1980 82.47 0.21176 0.20906 0.2128 0.26104 0.2584 RANDOM 53.699
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] -0.44 -0.27 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.471 r_dihedral_angle_4_deg 17.801 r_dihedral_angle_3_deg 15.896 r_long_range_B_refined 6.066 r_long_range_B_other 6.066 r_dihedral_angle_1_deg 5.853 r_mcangle_it 3.853 r_mcangle_other 3.853 r_scangle_it 3.46 r_scangle_other 3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.471 r_dihedral_angle_4_deg 17.801 r_dihedral_angle_3_deg 15.896 r_long_range_B_refined 6.066 r_long_range_B_other 6.066 r_dihedral_angle_1_deg 5.853 r_mcangle_it 3.853 r_mcangle_other 3.853 r_scangle_it 3.46 r_scangle_other 3.46 r_mcbond_it 2.29 r_mcbond_other 2.285 r_scbond_it 1.992 r_scbond_other 1.991 r_angle_refined_deg 1.311 r_angle_other_deg 0.928 r_symmetry_vdw_other 0.268 r_symmetry_hbond_refined 0.196 r_symmetry_vdw_refined 0.187 r_nbd_refined 0.174 r_nbtor_refined 0.162 r_nbd_other 0.136 r_xyhbond_nbd_refined 0.115 r_nbtor_other 0.072 r_chiral_restr 0.069 r_ncsr_local_group_1 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11092 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing