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Crystal structure of O-acetyl-L-homoserine sulfhydrolase from Saccharomyces cerevisiae in complex with Pyridoxal-5'-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 22% (w/v) PEG 6000, 200 mM LiCl, and 100 mM sodium acetate, pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.579 α = 90 b = 118.218 β = 92.908 c = 131.381 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2022-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.17 49.59 97.46 0.18 0.99 7.7 6.5 629183
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.21 1.6
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 2.171 49.59 96652 4833 97.447 0.175 0.1715 0.1763 0.2376 0.2384 52.594
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] -0.078 0.034 -0.051 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.866 r_dihedral_angle_3_deg 15.562 r_lrange_other 11.263 r_lrange_it 11.257 r_scangle_it 8.852 r_scangle_other 8.852 r_dihedral_angle_2_deg 7.834 r_dihedral_angle_1_deg 7.643 r_mcangle_other 7.343 r_mcangle_it 7.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.866 r_dihedral_angle_3_deg 15.562 r_lrange_other 11.263 r_lrange_it 11.257 r_scangle_it 8.852 r_scangle_other 8.852 r_dihedral_angle_2_deg 7.834 r_dihedral_angle_1_deg 7.643 r_mcangle_other 7.343 r_mcangle_it 7.342 r_scbond_it 6.072 r_scbond_other 6.071 r_mcbond_it 5.224 r_mcbond_other 5.22 r_angle_refined_deg 1.592 r_angle_other_deg 0.516 r_symmetry_nbd_refined 0.329 r_nbd_other 0.221 r_nbd_refined 0.22 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_refined 0.07 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12380 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing