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Ayg1p active site converted to tetrahedral sulfonate ester
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QD1 Ayg1p from A. fumigatus catalyzes polyketide shortening in the biosynthesis of DHN-melanin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 150 mM K/Na tartrate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.64 α = 90 b = 107.55 β = 90.01 c = 92.54 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 2021-01-31 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) 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 1.8 50 95.9 0.066 9.4 2.8 148659
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 1.8 1.9 97.4 0.546 1.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 46.49 141275 7356 95.87 0.23586 0.23529 0.2763 0.24649 0.2918 RANDOM 26.806
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] -14.57 4.68 37.59 -23.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.955 r_dihedral_angle_3_deg 13.228 r_dihedral_angle_4_deg 11.517 r_dihedral_angle_1_deg 6.5 r_long_range_B_refined 3.085 r_long_range_B_other 3.023 r_mcangle_it 1.651 r_mcangle_other 1.651 r_angle_refined_deg 1.287 r_scangle_other 1.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.955 r_dihedral_angle_3_deg 13.228 r_dihedral_angle_4_deg 11.517 r_dihedral_angle_1_deg 6.5 r_long_range_B_refined 3.085 r_long_range_B_other 3.023 r_mcangle_it 1.651 r_mcangle_other 1.651 r_angle_refined_deg 1.287 r_scangle_other 1.274 r_angle_other_deg 1.128 r_mcbond_it 1.058 r_mcbond_other 1.058 r_scbond_it 0.816 r_scbond_other 0.816 r_chiral_restr 0.051 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12344 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing