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Sesterterpene Synthase from Streptomyces mobaraensis (Sestermobaraene Synthase, SmTS1, apo)
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 6.5 293 100 mM Mes, 0.2 M MgCl2, 10% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.82 α = 101.63 b = 81.56 β = 97.98 c = 98.72 γ = 93.9
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 2024-09-08 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 1.7 30 94.9 0.066 10.5 3.2 235171
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 1.7 1.8 96 0.743 3.2
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 1.7 30 223391 11757 94.88 0.16412 0.16211 0.1743 0.20242 0.2109 RANDOM 26.332
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] 1.16 0.95 0.25 -0.36 -0.9 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.145 r_dihedral_angle_4_deg 15.912 r_dihedral_angle_3_deg 13.089 r_dihedral_angle_1_deg 5.367 r_long_range_B_refined 3.096 r_long_range_B_other 2.909 r_scangle_other 2.254 r_mcangle_it 2.149 r_mcangle_other 2.149 r_scbond_it 1.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.145 r_dihedral_angle_4_deg 15.912 r_dihedral_angle_3_deg 13.089 r_dihedral_angle_1_deg 5.367 r_long_range_B_refined 3.096 r_long_range_B_other 2.909 r_scangle_other 2.254 r_mcangle_it 2.149 r_mcangle_other 2.149 r_scbond_it 1.721 r_scbond_other 1.721 r_mcbond_it 1.603 r_mcbond_other 1.602 r_angle_other_deg 1.245 r_angle_refined_deg 1.181 r_rigid_bond_restr 0.778 r_chiral_restr 0.061 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 15357 Nucleic Acid Atoms Solvent Atoms 1044 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing