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Crystal structure of beta-ketoadipyl-CoA thiolase mutant (H356A) in complex hexanoyl coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 299 lithium chloride,PEG 6000,tris (pH- 7.3-8.3)
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.393 α = 90 b = 116.397 β = 90 c = 127.902 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2017-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.96 80 95.8 0.113 0.136 0.992 8.52 3.16 220195 19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.08 94.7 0.517 0.624 0.742 2.42 3.04
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Native structure 1.96 19.94 112475 968 95.29 0.1761 0.17581 0.20815 0.184 RANDOM 21.883
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] -0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.696 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_1_deg 6.968 r_long_range_B_refined 5.157 r_scbond_it 2.65 r_mcangle_it 2.15 r_angle_refined_deg 1.493 r_mcbond_it 1.477 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.696 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_1_deg 6.968 r_long_range_B_refined 5.157 r_scbond_it 2.65 r_mcangle_it 2.15 r_angle_refined_deg 1.493 r_mcbond_it 1.477 r_chiral_restr 0.109 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 11689 Nucleic Acid Atoms Solvent Atoms 1216 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Auto-Rickshaw phasing