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Crystal Structure of the acyltransferase domain from the eighth module of the spinosad polyketide synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1 M citric acid pH 5.0, 0.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.74 67.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.345 α = 90 b = 154.723 β = 92.09 c = 65.209 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2021-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 3.25 50 96.4 0.125 0.149 0.08 0.947 4.8 3.1 29154
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.31 97.7 0.435 0.519 0.279 0.811 3.1
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 3.26 50 26991 1385 93.23 0.20079 0.19786 0.2069 0.25752 0.2642 RANDOM 74.279
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] -2.27 0.7 -2.43 4.64
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 20.164 r_long_range_B_refined 20.163 r_dihedral_angle_3_deg 16.725 r_scangle_other 14.59 r_mcangle_it 10.899 r_mcangle_other 10.899 r_scbond_it 9.834 r_scbond_other 9.833 r_mcbond_it 7.294 r_mcbond_other 7.278
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 20.164 r_long_range_B_refined 20.163 r_dihedral_angle_3_deg 16.725 r_scangle_other 14.59 r_mcangle_it 10.899 r_mcangle_other 10.899 r_scbond_it 9.834 r_scbond_other 9.833 r_mcbond_it 7.294 r_mcbond_other 7.278 r_dihedral_angle_2_deg 6.903 r_dihedral_angle_1_deg 6.887 r_angle_refined_deg 1.09 r_angle_other_deg 0.345 r_chiral_restr 0.048 r_gen_planes_refined 0.01 r_bond_refined_d 0.005 r_gen_planes_other 0.002 r_bond_other_d r_dihedral_angle_4_deg 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 9299 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing