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Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 295 100 mM HEPES, pH 6.4, 18% PEG3350, 250 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.16 α = 90 b = 81.94 β = 125.81 c = 96.81 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-F 2013-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.95 29.64 98.4 0.05 0.03 0.99 15.7 3.4 60799 3 34.8
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 1.95 2.05 99.3 0.42 0.22 0.87 2.94 3.4
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 3ZBG 1.95 29.64 57744 3040 98.73 0.17131 0.16943 0.1772 0.20702 0.2128 RANDOM 34.182
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] 0.19 0.97 0.22 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.815 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_4_deg 12.675 r_dihedral_angle_1_deg 6.088 r_long_range_B_refined 5.212 r_long_range_B_other 5.212 r_scangle_it 4.301 r_scangle_other 4.3 r_scbond_it 2.822 r_scbond_other 2.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.815 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_4_deg 12.675 r_dihedral_angle_1_deg 6.088 r_long_range_B_refined 5.212 r_long_range_B_other 5.212 r_scangle_it 4.301 r_scangle_other 4.3 r_scbond_it 2.822 r_scbond_other 2.822 r_mcangle_it 2.801 r_mcangle_other 2.8 r_mcbond_other 2.032 r_mcbond_it 2.031 r_angle_refined_deg 1.498 r_angle_other_deg 0.95 r_nbd_refined 0.209 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.166 r_nbd_other 0.154 r_symmetry_vdw_other 0.15 r_xyhbond_nbd_refined 0.128 r_symmetry_vdw_refined 0.106 r_chiral_restr 0.08 r_nbtor_other 0.076 r_xyhbond_nbd_other 0.048 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5860 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing