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Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-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-methylglyceryl-CoA, 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.53 51.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.768 α = 90 b = 146.493 β = 90 c = 174.321 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 2022-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 1.551 84.68 92.3 0.102 1 18.7 13.8 104204
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 1.551 1.694 72.2 1.682 0.64 1.6 13.3
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 1.551 84.68 104204 5203 54.642 0.159 0.1577 0.1576 0.1841 0.1842 22.955
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] -0.064 0.139 -0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.146 r_dihedral_angle_3_deg 11.765 r_dihedral_angle_1_deg 6.397 r_dihedral_angle_2_deg 6.048 r_lrange_it 5.91 r_scangle_it 3.607 r_scbond_it 2.444 r_mcangle_it 1.87 r_angle_refined_deg 1.789 r_mcbond_it 1.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.146 r_dihedral_angle_3_deg 11.765 r_dihedral_angle_1_deg 6.397 r_dihedral_angle_2_deg 6.048 r_lrange_it 5.91 r_scangle_it 3.607 r_scbond_it 2.444 r_mcangle_it 1.87 r_angle_refined_deg 1.789 r_mcbond_it 1.269 r_nbtor_refined 0.309 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.193 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.162 r_chiral_restr 0.113 r_ncsr_local_group_1 0.053 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8618 Nucleic Acid Atoms Solvent Atoms 1065 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing