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Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with 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 HEPES, pH
7.0, 15 % PEG3350,
250 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.96 α = 90 b = 80.88 β = 126.29 c = 96.47 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 2M 2015-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9174 Diamond I04-1
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 1.46 47.59 98.2 0.11 0.04 0.998 13.7 7.5 140415 2.9 18.4
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 1.46 1.56 98.2 0.68 0.19 0.856 2.85 7.5
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 6HRV 1.46 47.59 133408 7005 98.46 0.15736 0.15648 0.1559 0.17423 0.174 RANDOM 14.128
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] -0.2 0.35 -0.25 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.563 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_4_deg 11.699 r_dihedral_angle_1_deg 6.421 r_long_range_B_other 4.43 r_long_range_B_refined 4.429 r_scangle_it 3.236 r_scangle_other 3.236 r_scbond_it 2.067 r_scbond_other 2.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.563 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_4_deg 11.699 r_dihedral_angle_1_deg 6.421 r_long_range_B_other 4.43 r_long_range_B_refined 4.429 r_scangle_it 3.236 r_scangle_other 3.236 r_scbond_it 2.067 r_scbond_other 2.067 r_mcangle_it 1.805 r_mcangle_other 1.805 r_angle_refined_deg 1.589 r_angle_other_deg 1.52 r_mcbond_it 1.154 r_mcbond_other 1.153 r_nbd_refined 0.222 r_nbd_other 0.178 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.159 r_symmetry_vdw_refined 0.156 r_symmetry_vdw_other 0.153 r_symmetry_hbond_refined 0.116 r_nbtor_other 0.083 r_chiral_restr 0.078 r_xyhbond_nbd_other 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5872 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing