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Sesterterpene Synthase from Streptomyces subrutilus (Subrutilane Synthase, SrS) in complex with the surrogate geranyl-farnesyl-thiopyrophosphate (GFSPP)
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 9 293 100 mM Bicine, 30% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.91 α = 90 b = 89.63 β = 91.1 c = 102.69 γ = 90
Symmetry Space Group P 1 21 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 2024-10-27 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 2.3 30 95 0.117 9.3 3.6 57484
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 2.3 2.4 96.4 0.87 2.8 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 2.3 30 54591 2874 95.01 0.18072 0.17909 0.1888 0.21103 0.2156 RANDOM 29.302
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] -0.36 0.51 -0.03 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.378 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 5.047 r_long_range_B_refined 1.963 r_long_range_B_other 1.912 r_angle_refined_deg 1.161 r_mcangle_it 1.158 r_mcangle_other 1.158 r_angle_other_deg 1.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.378 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 5.047 r_long_range_B_refined 1.963 r_long_range_B_other 1.912 r_angle_refined_deg 1.161 r_mcangle_it 1.158 r_mcangle_other 1.158 r_angle_other_deg 1.062 r_scangle_other 0.99 r_mcbond_it 0.8 r_mcbond_other 0.8 r_scbond_it 0.686 r_scbond_other 0.686 r_rigid_bond_restr 0.241 r_chiral_restr 0.042 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 10728 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing