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Stilbene synthase of Cenchrus americanus in complex with resveratrol
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 5 mM resveratrol, 10 %(v/v) PEG 400, 10 %(v/v) Glycerol, 0.7 M sodium citrate tribasic pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.68 66.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.345 α = 90 b = 137.422 β = 90 c = 179.102 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 EIGER X 16M 2024-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979 SSRF BL10U2
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 1.31 89.712 100 0.997 11.8 13.1 311348 16.4
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 1.31 1.38 99.6 0.434 1 11.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 89.712 253124 12640 99.966 0.162 0.1612 0.1618 0.1791 0.1799 22.604
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] -0.091 -0.587 0.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.011 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_2_deg 9.9 r_lrange_it 6.617 r_lrange_other 6.538 r_dihedral_angle_1_deg 6.431 r_scangle_it 5.562 r_scangle_other 5.562 r_scbond_it 3.719 r_scbond_other 3.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.011 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_2_deg 9.9 r_lrange_it 6.617 r_lrange_other 6.538 r_dihedral_angle_1_deg 6.431 r_scangle_it 5.562 r_scangle_other 5.562 r_scbond_it 3.719 r_scbond_other 3.718 r_mcangle_it 2.764 r_mcangle_other 2.764 r_angle_refined_deg 2.177 r_mcbond_it 2.023 r_mcbond_other 2.012 r_angle_other_deg 0.696 r_symmetry_nbd_refined 0.448 r_nbd_other 0.244 r_nbd_refined 0.231 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.157 r_chiral_restr 0.105 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.083 r_gen_planes_other 0.018 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6038 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing