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Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with a covalently bound reaction intermediate as well as products formyl-CoA and acetone
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 2 M ammonium sulfate,
0.1 M HEPES pH 7.0
1 mM 2-Hydroxyisobutyryl-CoA,
5 mM ADP,
5 mM MgCl2,
5 mM ThDP
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.234 α = 90 b = 116.234 β = 90 c = 312.056 γ = 120
Symmetry Space Group P 65 2 2
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 2021-03-11 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 1.64 100.662 96.8 0.189 0.03 0.999 15.3 40.1 98153
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 1.64 1.84 82.5 1.539 0.249 0.878 1.7 38.7
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 1.64 100.662 98152 4841 64.516 0.147 0.1452 0.1451 0.1751 0.175 19.878
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 0.01 0.02 -0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.622 r_dihedral_angle_4_deg 19.258 r_dihedral_angle_3_deg 12.047 r_dihedral_angle_1_deg 6.55 r_lrange_it 6.071 r_lrange_other 5.819 r_scangle_it 3.537 r_scangle_other 3.389 r_scbond_it 2.538 r_scbond_other 2.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.622 r_dihedral_angle_4_deg 19.258 r_dihedral_angle_3_deg 12.047 r_dihedral_angle_1_deg 6.55 r_lrange_it 6.071 r_lrange_other 5.819 r_scangle_it 3.537 r_scangle_other 3.389 r_scbond_it 2.538 r_scbond_other 2.417 r_mcangle_it 1.847 r_mcangle_other 1.847 r_angle_refined_deg 1.759 r_angle_other_deg 1.485 r_mcbond_it 1.212 r_mcbond_other 1.209 r_nbd_refined 0.215 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_other 0.184 r_xyhbond_nbd_refined 0.183 r_symmetry_nbd_refined 0.169 r_nbd_other 0.167 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.14 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.076 r_metal_ion_refined 0.026 r_bond_refined_d 0.014 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 8730 Nucleic Acid Atoms Solvent Atoms 1049 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction STARANISO data scaling MoRDa phasing