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Sesterterpene Synthase from Streptomyces violarus (Sesterviolene Synthase, SvSS, 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 7.5 293 100 mM BisTris, 0.2 M MgCl2, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.9 α = 92.36 b = 54.47 β = 102.84 c = 74.03 γ = 118.47
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 1.4 30 95.4 0.079 9.1 3.6 121250
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 1.4 1.5 93.5 0.69 2.2 3.5
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 1.4 30 115184 6062 95.41 0.16382 0.16284 0.1648 0.18231 0.1845 RANDOM 19.114
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] -0.62 -0.01 0.02 0.44 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.13 r_dihedral_angle_4_deg 16.639 r_dihedral_angle_3_deg 12.214 r_dihedral_angle_1_deg 4.986 r_long_range_B_refined 1.844 r_long_range_B_other 1.614 r_angle_other_deg 1.225 r_angle_refined_deg 1.142 r_scangle_other 0.922 r_mcangle_other 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.13 r_dihedral_angle_4_deg 16.639 r_dihedral_angle_3_deg 12.214 r_dihedral_angle_1_deg 4.986 r_long_range_B_refined 1.844 r_long_range_B_other 1.614 r_angle_other_deg 1.225 r_angle_refined_deg 1.142 r_scangle_other 0.922 r_mcangle_other 0.848 r_mcangle_it 0.847 r_scbond_it 0.697 r_scbond_other 0.697 r_mcbond_it 0.595 r_mcbond_other 0.595 r_rigid_bond_restr 0.318 r_chiral_restr 0.05 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 5314 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing