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Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with CoA and octanoyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 100 mM MOPS, pH 7.0,
10 % PEG6000, 20%
glycerol
Crystal Properties Matthews coefficient Solvent content 2.3 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.18 α = 90 b = 81.32 β = 126.08 c = 96.63 γ = 90
Symmetry Space Group C 1 2 1
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 2015-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.2822 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.73 42.88 99.1 0.09 0.06 0.996 8.42 3.2 85694 -3 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.83 97.6 0.63 0.38 0.403 2.6
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 MOLECULAR REPLACEMENT THROUGHOUT 6HRV 1.73 42.88 81387 4301 99.38 0.19192 0.19006 0.1866 0.22733 0.2202 RANDOM 34.337
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] 0.61 0.24 0.75 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.086 r_dihedral_angle_4_deg 14.915 r_dihedral_angle_3_deg 13.048 r_long_range_B_refined 6.085 r_long_range_B_other 6.083 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.808 r_scangle_other 4.808 r_scbond_it 3.192 r_scbond_other 3.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.086 r_dihedral_angle_4_deg 14.915 r_dihedral_angle_3_deg 13.048 r_long_range_B_refined 6.085 r_long_range_B_other 6.083 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.808 r_scangle_other 4.808 r_scbond_it 3.192 r_scbond_other 3.191 r_mcangle_it 2.797 r_mcangle_other 2.797 r_mcbond_it 2.089 r_mcbond_other 2.084 r_angle_refined_deg 1.558 r_angle_other_deg 1.064 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.19 r_nbtor_refined 0.174 r_symmetry_vdw_other 0.159 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.122 r_symmetry_vdw_refined 0.12 r_chiral_restr 0.096 r_nbtor_other 0.076 r_xyhbond_nbd_other 0.03 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5853 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing