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Sesterterpene Synthase from Kitasatospora viridis in complex with the surrogate GFSPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RRZ Sesterterpene Synthase from Kitasatospora viridis (apo)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.1 M PCB buffer, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.19 α = 90 b = 97.19 β = 90 c = 70.96 γ = 90
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 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 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 96 0.096 8 2.6 28407
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 0.729 1.7 2.4
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 2.3 30 26978 1420 96.05 0.19485 0.19259 0.2015 0.23801 0.2427 RANDOM 42.282
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] -0.18 -0.18 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.846 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_4_deg 14.297 r_dihedral_angle_1_deg 4.563 r_long_range_B_refined 2.34 r_long_range_B_other 2.267 r_mcangle_it 1.449 r_mcangle_other 1.449 r_scangle_other 1.217 r_angle_refined_deg 1.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.846 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_4_deg 14.297 r_dihedral_angle_1_deg 4.563 r_long_range_B_refined 2.34 r_long_range_B_other 2.267 r_mcangle_it 1.449 r_mcangle_other 1.449 r_scangle_other 1.217 r_angle_refined_deg 1.178 r_angle_other_deg 1.045 r_mcbond_it 0.991 r_mcbond_other 0.984 r_scbond_it 0.812 r_scbond_other 0.811 r_rigid_bond_restr 0.218 r_chiral_restr 0.04 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 5404 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing