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Sesterterpene Synthase from Kitasatospora viridis (V57L-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 6.5 277 1.6 M tri-Sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.23 61.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.76 α = 90 b = 95.76 β = 90 c = 112.3 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 99.8 0.072 16.3 7.5 63132
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 0.751 3 7.8
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 59963 3156 99.73 0.15297 0.15172 0.1667 0.17676 0.1869 RANDOM 25.288
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] -0.76 -0.76 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.771 r_dihedral_angle_4_deg 13.945 r_dihedral_angle_3_deg 12.987 r_dihedral_angle_1_deg 5.268 r_long_range_B_refined 2.706 r_long_range_B_other 2.446 r_angle_other_deg 1.215 r_mcangle_it 1.215 r_mcangle_other 1.215 r_angle_refined_deg 1.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.771 r_dihedral_angle_4_deg 13.945 r_dihedral_angle_3_deg 12.987 r_dihedral_angle_1_deg 5.268 r_long_range_B_refined 2.706 r_long_range_B_other 2.446 r_angle_other_deg 1.215 r_mcangle_it 1.215 r_mcangle_other 1.215 r_angle_refined_deg 1.146 r_scangle_other 1.131 r_mcbond_it 0.871 r_mcbond_other 0.87 r_scbond_it 0.833 r_scbond_other 0.833 r_rigid_bond_restr 0.375 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 2737 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing