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Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493Q structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG 1500,
0.1 M MIB buffer pH 7.0,
5 mM 3-deazathiamin diphosphate,
1 mM 2-Hydroxybutyryl-CoA,
5 mM MgCl2,
5 mM ADP
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.674 α = 90 b = 145.481 β = 90 c = 174.198 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 16M 2021-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.762 87.099 95.4 0.103 0.031 0.999 15 11.9 83716
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 1.762 1.961 71.5 1.382 0.433 0.736 1.7 11.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.762 87.099 83716 4266 64.65 0.149 0.1466 0.1457 0.1854 0.1836 26.748
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] -0.106 0.095 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.708 r_dihedral_angle_4_deg 19.203 r_dihedral_angle_3_deg 13.824 r_dihedral_angle_1_deg 6.848 r_lrange_it 5.142 r_lrange_other 4.978 r_scangle_it 3.057 r_scangle_other 3.057 r_scbond_it 1.989 r_scbond_other 1.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.708 r_dihedral_angle_4_deg 19.203 r_dihedral_angle_3_deg 13.824 r_dihedral_angle_1_deg 6.848 r_lrange_it 5.142 r_lrange_other 4.978 r_scangle_it 3.057 r_scangle_other 3.057 r_scbond_it 1.989 r_scbond_other 1.988 r_angle_refined_deg 1.849 r_mcangle_it 1.844 r_mcangle_other 1.844 r_angle_other_deg 1.445 r_mcbond_it 1.229 r_mcbond_other 1.228 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.196 r_nbd_other 0.187 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_nbd_refined 0.162 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.098 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.059 r_metal_ion_refined 0.025 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8602 Nucleic Acid Atoms Solvent Atoms 1003 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing