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Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493D structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG 1500, 0.1 M MIB buffer pH 7.0, 5 mM 3-deazathiamin diphosphate, 1 mM 2-Hydroxyisobutyryl-CoA, 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.98 α = 90 b = 147.528 β = 90 c = 174.449 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 2021-07-15 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) 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 1.63 87.23 94.7 0.13 1 12.7 11.6 83484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.83 67.4 1.669 0.7 1.7 11.4
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.63 87.225 83483 4194 50.235 0.159 0.1574 0.1574 0.1928 0.1929 24.261
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] 0.096 -0.277 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.582 r_dihedral_angle_3_deg 12.305 r_dihedral_angle_1_deg 6.379 r_dihedral_angle_2_deg 6.098 r_lrange_it 5.409 r_scangle_it 3.6 r_scbond_it 2.391 r_mcangle_it 1.927 r_angle_refined_deg 1.673 r_mcbond_it 1.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.582 r_dihedral_angle_3_deg 12.305 r_dihedral_angle_1_deg 6.379 r_dihedral_angle_2_deg 6.098 r_lrange_it 5.409 r_scangle_it 3.6 r_scbond_it 2.391 r_mcangle_it 1.927 r_angle_refined_deg 1.673 r_mcbond_it 1.307 r_nbtor_refined 0.304 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.164 r_symmetry_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.135 r_chiral_restr 0.109 r_ncsr_local_group_1 0.049 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8609 Nucleic Acid Atoms Solvent Atoms 991 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing