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Sesterterpene Synthase from Streptomyces mobaraensis (Sestermobaraene Synthase, SmTS1) in complex with pyrophosphate (PPi)
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 7.5 293 100 mM Tris, 0.15 M MgCl2, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.71 54.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.44 α = 90 b = 228.69 β = 90 c = 63.06 γ = 90
Symmetry Space Group P 21 21 2
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 2022-09-10 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 2.8 30 97.8 0.05 16.7 4.2 64377
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 2.8 2.9 98.8 0.667 2.1 4.4
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 2.8 30 61073 3214 97.73 0.22788 0.22657 0.2385 0.25194 0.2722 RANDOM 98.543
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] -11.94 -9.82 21.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.302 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_4_deg 14.826 r_long_range_B_refined 5.216 r_long_range_B_other 5.131 r_dihedral_angle_1_deg 4.491 r_mcangle_it 1.851 r_mcangle_other 1.851 r_scangle_other 1.467 r_mcbond_it 1.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.302 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_4_deg 14.826 r_long_range_B_refined 5.216 r_long_range_B_other 5.131 r_dihedral_angle_1_deg 4.491 r_mcangle_it 1.851 r_mcangle_other 1.851 r_scangle_other 1.467 r_mcbond_it 1.366 r_mcbond_other 1.366 r_angle_refined_deg 1.143 r_angle_other_deg 1.029 r_scbond_it 1.016 r_scbond_other 1.015 r_rigid_bond_restr 0.736 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 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 16171 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing