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Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) 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 4RJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG 1500,
0.1 M MIB buffer (sodium malonate dibasic monohydrate, imidazole, boric acid) pH 6.0
5 mM 3-deazathiamin diphosphate,
1 mM 2-Hydroxyisobutyryl-CoA,
5 mM MgCl2,
5 mM ADP
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.95 α = 90 b = 146.138 β = 90 c = 174.749 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) 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 1.553 87.374 89.4 0.114 0.035 0.999 10.1 11.4 100209
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 1.553 1.752 60.9 1.537 0.473 0.644 1.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4RJI 1.553 87.374 100208 5011 52.676 0.161 0.1595 0.1614 0.1936 0.1945 20.939
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] -0.347 0.443 -0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.944 r_dihedral_angle_4_deg 18.798 r_dihedral_angle_3_deg 13.156 r_dihedral_angle_1_deg 6.879 r_lrange_it 4.685 r_lrange_other 4.494 r_scangle_it 2.96 r_scangle_other 2.96 r_scbond_it 1.944 r_scbond_other 1.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.944 r_dihedral_angle_4_deg 18.798 r_dihedral_angle_3_deg 13.156 r_dihedral_angle_1_deg 6.879 r_lrange_it 4.685 r_lrange_other 4.494 r_scangle_it 2.96 r_scangle_other 2.96 r_scbond_it 1.944 r_scbond_other 1.944 r_mcangle_other 1.891 r_mcangle_it 1.89 r_angle_refined_deg 1.853 r_angle_other_deg 1.514 r_mcbond_it 1.257 r_mcbond_other 1.255 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.193 r_nbd_other 0.187 r_symmetry_nbd_other 0.181 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.12 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_1 0.059 r_xyhbond_nbd_other 0.043 r_metal_ion_refined 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 1017 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MoRDa phasing