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Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A 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 SPG buffer pH 6.0,
5 mM 3-deaza-ThDP,
1 mM 2-hydroxybutyryl-CoA,
5 mM MgCl2,
5 mM ADP
Crystal Properties Matthews coefficient Solvent content 2.54 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.915 α = 90 b = 146.718 β = 90 c = 174.413 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 1.625 87.207 94.8 0.103 0.031 0.999 14.2 11.8 102472
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 1.625 1.78 1.624 0.481 0.686 1.5
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 1.625 87.206 102471 5146 61.458 0.155 0.1537 0.1527 0.1858 0.1843 22.029
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] -0.086 0.154 -0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.584 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 13.643 r_dihedral_angle_1_deg 6.922 r_lrange_it 4.944 r_lrange_other 4.752 r_scangle_it 3.108 r_scangle_other 3.107 r_scbond_it 2.046 r_scbond_other 2.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.584 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 13.643 r_dihedral_angle_1_deg 6.922 r_lrange_it 4.944 r_lrange_other 4.752 r_scangle_it 3.108 r_scangle_other 3.107 r_scbond_it 2.046 r_scbond_other 2.046 r_mcangle_it 1.931 r_mcangle_other 1.931 r_angle_refined_deg 1.778 r_angle_other_deg 1.502 r_mcbond_it 1.296 r_mcbond_other 1.287 r_nbd_refined 0.218 r_nbd_other 0.194 r_symmetry_nbd_other 0.183 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.139 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.057 r_metal_ion_refined 0.033 r_xyhbond_nbd_other 0.015 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8594 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing