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Sesterterpene Synthase from Streptomyces violarus (Sesterviolene Synthase, SvSS) in complex with the surrogate 2,3-dihydro-geranyl-farnesyl-pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 29MK Sesterterpene Synthase from Streptomyces violarus (Sesterviolene Synthase, SvSS, apo)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 100 mM Tris, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.9 α = 100.62 b = 98.21 β = 113.36 c = 98.2 γ = 112.15
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 2025-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.85 30 97.1 0.062 11.2 3.6 198778
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 1.85 1.95 96.5 0.749 1.9 3.7
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 1.85 30 188814 9937 97.29 0.18033 0.17827 0.19 0.21919 0.2256 RANDOM 37.685
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] 0.5 0.49 -0.16 -0.14 -0.12 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.72 r_dihedral_angle_4_deg 18.119 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.458 r_long_range_B_refined 3.344 r_long_range_B_other 3.306 r_scangle_other 2.675 r_mcangle_it 2.653 r_mcangle_other 2.652 r_scbond_it 2.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.72 r_dihedral_angle_4_deg 18.119 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.458 r_long_range_B_refined 3.344 r_long_range_B_other 3.306 r_scangle_other 2.675 r_mcangle_it 2.653 r_mcangle_other 2.652 r_scbond_it 2.026 r_scbond_other 2.026 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_other_deg 1.234 r_angle_refined_deg 1.223 r_rigid_bond_restr 0.735 r_chiral_restr 0.057 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15923 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing