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Stilbene synthase of Cenchrus americanus co-crystallized with p-coumaroyl-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 3.82 67.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.19 α = 90 b = 139.47 β = 90 c = 180.65 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 S 6M 2022-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.88 47.48 99.5 0.996 9.61 11.45 106865 21.4
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 1.88 2 0.486
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 1.882 47.48 106865 2100 99.505 0.188 0.1873 0.1985 0.2172 0.2257 29.057
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] -1.396 1.474 -0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.496 r_dihedral_angle_3_deg 14.791 r_dihedral_angle_2_deg 11.977 r_lrange_other 10.833 r_lrange_it 10.826 r_scangle_it 9.161 r_scangle_other 9.16 r_dihedral_angle_1_deg 7.234 r_scbond_it 6.091 r_scbond_other 6.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.496 r_dihedral_angle_3_deg 14.791 r_dihedral_angle_2_deg 11.977 r_lrange_other 10.833 r_lrange_it 10.826 r_scangle_it 9.161 r_scangle_other 9.16 r_dihedral_angle_1_deg 7.234 r_scbond_it 6.091 r_scbond_other 6.09 r_mcangle_other 3.884 r_mcangle_it 3.881 r_mcbond_it 2.977 r_mcbond_other 2.973 r_angle_refined_deg 2.439 r_angle_other_deg 0.796 r_symmetry_xyhbond_nbd_refined 0.235 r_nbd_refined 0.22 r_symmetry_nbd_other 0.204 r_symmetry_nbd_refined 0.203 r_nbd_other 0.199 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.088 r_dihedral_angle_other_2_deg 0.025 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 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 389 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing