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Stilbene synthase of Cenchrus americanus co-crystallized with p-coumaroyl-CoA and malonyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.25 M sodium citrate tribasic, 0.1 M HEPES pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.74 67.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.54 α = 90 b = 138.15 β = 90 c = 179.96 γ = 90
Symmetry Space Group I 2 2 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 PILATUS3 2M 2022-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.77 47.18 100 0.998 11.63 13.39 126334 30.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.88 0.413
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.77 47.18 126334 2100 99.986 0.1721 0.1854 0.1905 0.2026 27.843
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] -1.346 0.89 0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.514 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_2_deg 7.77 r_lrange_it 7.348 r_lrange_other 7.325 r_dihedral_angle_1_deg 6.669 r_scangle_it 6.123 r_scangle_other 6.123 r_scbond_other 4.314 r_scbond_it 4.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.514 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_2_deg 7.77 r_lrange_it 7.348 r_lrange_other 7.325 r_dihedral_angle_1_deg 6.669 r_scangle_it 6.123 r_scangle_other 6.123 r_scbond_other 4.314 r_scbond_it 4.311 r_mcangle_other 3.271 r_mcangle_it 3.267 r_mcbond_other 2.407 r_mcbond_it 2.406 r_angle_refined_deg 1.944 r_angle_other_deg 0.65 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.218 r_nbd_other 0.201 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.177 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.081 r_dihedral_angle_other_2_deg 0.021 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6072 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing