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Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A 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 51.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.857 α = 90 b = 145.789 β = 90 c = 174.337 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 1.72 87.17 94 0.193 1 11.2 13.5 80334
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 1.72 1.89 71.8 1.908 0.6 1.6 12.9
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 1.72 87.168 80327 4076 57.499 0.164 0.1618 0.1618 0.2036 0.2036 26.507
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] -0.319 0.56 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.402 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 6.451 r_lrange_it 6.064 r_dihedral_angle_2_deg 5.415 r_scangle_it 3.502 r_scbond_it 2.368 r_mcangle_it 2.025 r_angle_refined_deg 1.617 r_mcbond_it 1.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.402 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 6.451 r_lrange_it 6.064 r_dihedral_angle_2_deg 5.415 r_scangle_it 3.502 r_scbond_it 2.368 r_mcangle_it 2.025 r_angle_refined_deg 1.617 r_mcbond_it 1.333 r_nbtor_refined 0.308 r_nbd_refined 0.209 r_symmetry_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.177 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.104 r_ncsr_local_group_1 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8610 Nucleic Acid Atoms Solvent Atoms 1043 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing