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Purification,crystallization and structural analysis of cytoplastic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 0.2M ammonium citrate (pH 6.5), polyethylene glycol 3350 (19%)
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.804 α = 90 b = 89.25 β = 90 c = 119.189 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 6M 2017-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97778 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.93 50 98.8 0.1 0.034 18.7 8.8 62459 15.6
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 1.93 1.98 98.1 0.515 0.183 0.946 5.1 8.3
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 2IB7 1.93 47.53 59159 3263 97.04 0.15655 0.15572 0.1604 0.17181 0.1776 RANDOM 22.7
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] 0.4 -1.41 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.811 r_dihedral_angle_4_deg 14.548 r_dihedral_angle_3_deg 13.541 r_dihedral_angle_1_deg 5.615 r_angle_refined_deg 1.252 r_angle_other_deg 0.902 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_bond_other_d 0.006 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.811 r_dihedral_angle_4_deg 14.548 r_dihedral_angle_3_deg 13.541 r_dihedral_angle_1_deg 5.615 r_angle_refined_deg 1.252 r_angle_other_deg 0.902 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5834 Nucleic Acid Atoms Solvent Atoms 809 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-2000 data scaling MOLREP phasing