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Crystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant with acetoacetyl-CoA.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 100 mM Bis Tris propane, pH 7.5, 0.2M sodium fluoride and 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.141 α = 90 b = 89.804 β = 104.76 c = 123.716 γ = 90
Symmetry Space Group P 1 21 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 2014-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976250 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.98 119.63 99.2 0.15 0.99 6.9 3.8 108328 16.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 99.1 0.72 0.57 2 3.9
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 3ZBN 1.98 119.63 103007 5300 99.14 0.19113 0.18934 0.1964 0.22607 0.2311 RANDOM 25.087
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] 1.19 0.34 -1.46 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.939 r_dihedral_angle_4_deg 17.973 r_dihedral_angle_3_deg 14.585 r_long_range_B_refined 7.091 r_long_range_B_other 7.09 r_dihedral_angle_1_deg 6.447 r_scangle_other 5.11 r_mcangle_it 3.358 r_mcangle_other 3.358 r_scbond_it 3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.939 r_dihedral_angle_4_deg 17.973 r_dihedral_angle_3_deg 14.585 r_long_range_B_refined 7.091 r_long_range_B_other 7.09 r_dihedral_angle_1_deg 6.447 r_scangle_other 5.11 r_mcangle_it 3.358 r_mcangle_other 3.358 r_scbond_it 3.21 r_scbond_other 3.21 r_mcbond_it 2.145 r_mcbond_other 2.144 r_angle_refined_deg 1.852 r_angle_other_deg 1.652 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.01 r_gen_planes_other 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12892 Nucleic Acid Atoms Solvent Atoms 830 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing