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Ayg1p in complex with 1,3-Dihydroxynaphthalene
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 293 100 mM K/Na tartrate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.47 α = 90 b = 107.48 β = 90.14 c = 92.51 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 2021-08-29 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 1.75 50 94.8 0.109 6.5 3.1 159406
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 1.75 1.85 96.2 0.614 2.1
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 1.75 46.47 151446 7932 94.28 0.22909 0.2286 0.2414 0.23865 0.2519 RANDOM 20.861
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] -2.8 -1.34 19.64 -16.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.991 r_dihedral_angle_3_deg 12.763 r_dihedral_angle_4_deg 12.298 r_dihedral_angle_1_deg 6.382 r_long_range_B_refined 2.759 r_long_range_B_other 2.527 r_angle_refined_deg 1.211 r_angle_other_deg 1.171 r_mcangle_it 1.081 r_mcangle_other 1.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.991 r_dihedral_angle_3_deg 12.763 r_dihedral_angle_4_deg 12.298 r_dihedral_angle_1_deg 6.382 r_long_range_B_refined 2.759 r_long_range_B_other 2.527 r_angle_refined_deg 1.211 r_angle_other_deg 1.171 r_mcangle_it 1.081 r_mcangle_other 1.081 r_scangle_other 1.038 r_mcbond_it 0.649 r_mcbond_other 0.648 r_scbond_it 0.634 r_scbond_other 0.634 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 12406 Nucleic Acid Atoms Solvent Atoms 1198 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing