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Sesterterpene Synthase from Streptomyces sp. Tue 2975 (Sesterviolene Synthase, StSS, apo)
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 5.5 293 100 mM BisTris, 0.1 M MgCl2, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75 α = 90 b = 79.64 β = 103.58 c = 129.6 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 EIGER X 16M 2025-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 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 2.2 30 98.3 0.059 17 3.4 37113
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 2.2 2.3 97.2 0.692 2.5 3.4
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 2.2 30 35243 1855 98.29 0.17551 0.17311 0.1825 0.21948 0.2263 RANDOM 42.369
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] -0.83 -1.86 2.71 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.386 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 13.821 r_dihedral_angle_1_deg 5.43 r_long_range_B_refined 4.58 r_long_range_B_other 4.575 r_mcangle_it 3.427 r_mcangle_other 3.427 r_scangle_other 3.243 r_mcbond_it 2.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.386 r_dihedral_angle_4_deg 19.531 r_dihedral_angle_3_deg 13.821 r_dihedral_angle_1_deg 5.43 r_long_range_B_refined 4.58 r_long_range_B_other 4.575 r_mcangle_it 3.427 r_mcangle_other 3.427 r_scangle_other 3.243 r_mcbond_it 2.423 r_mcbond_other 2.422 r_scbond_it 2.354 r_scbond_other 2.354 r_angle_refined_deg 1.19 r_angle_other_deg 1.162 r_rigid_bond_restr 0.752 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 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 5124 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing