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Sesterterpene Synthase from Kitasatospora viridis (I303Y-Variant, apo)
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 7.5 277 0.1 M HEPES, 1.4 M tri-sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.27 62.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.53 α = 90 b = 95.53 β = 90 c = 114.4 γ = 90
Symmetry Space Group P 41 21 2
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 2024-11-23 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 1.65 30 99.7 0.068 18.2 7.3 63976
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 1.65 1.75 99.9 0.798 3.1 7.3
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 1.65 30 60770 3198 99.71 0.15799 0.15687 0.1573 0.1794 0.1799 RANDOM 22.587
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] -0.35 -0.35 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.227 r_dihedral_angle_4_deg 14.578 r_dihedral_angle_3_deg 12.998 r_dihedral_angle_1_deg 4.948 r_long_range_B_refined 2.403 r_long_range_B_other 2.082 r_angle_other_deg 1.22 r_angle_refined_deg 1.162 r_mcangle_it 1.138 r_mcangle_other 1.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.227 r_dihedral_angle_4_deg 14.578 r_dihedral_angle_3_deg 12.998 r_dihedral_angle_1_deg 4.948 r_long_range_B_refined 2.403 r_long_range_B_other 2.082 r_angle_other_deg 1.22 r_angle_refined_deg 1.162 r_mcangle_it 1.138 r_mcangle_other 1.137 r_scangle_other 1.076 r_mcbond_it 0.793 r_mcbond_other 0.793 r_scbond_it 0.763 r_scbond_other 0.763 r_rigid_bond_restr 0.339 r_chiral_restr 0.057 r_gen_planes_refined 0.004 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 2695 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing