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AntI in complex with 1-Naphthol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other 6HXA AntI from P. luminescens catalyses terminal polyketide shortening in the biosynthesis of anthraquinones
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 100 mM HEPES pH 7.9, 0.1 M NaAc pH 6.6, 24% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.94 α = 90 b = 154.73 β = 90 c = 92.09 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 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 2.05 50 95.8 0.045 17.29 4.5 24440
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 2.05 2.15 0.669 3.8
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 2.05 45.68 23215 1221 95.76 0.19242 0.19164 0.1923 0.2072 0.2088 RANDOM 51.634
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] 36.38 -18.83 -17.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.724 r_dihedral_angle_4_deg 14.282 r_dihedral_angle_3_deg 12.262 r_dihedral_angle_1_deg 5.48 r_long_range_B_refined 2.106 r_long_range_B_other 2.105 r_mcangle_it 1.322 r_mcangle_other 1.322 r_angle_refined_deg 1.14 r_scangle_other 1.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.724 r_dihedral_angle_4_deg 14.282 r_dihedral_angle_3_deg 12.262 r_dihedral_angle_1_deg 5.48 r_long_range_B_refined 2.106 r_long_range_B_other 2.105 r_mcangle_it 1.322 r_mcangle_other 1.322 r_angle_refined_deg 1.14 r_scangle_other 1.088 r_angle_other_deg 1.07 r_mcbond_it 0.91 r_mcbond_other 0.91 r_scbond_it 0.766 r_scbond_other 0.765 r_rigid_bond_restr 0.224 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2993 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing