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Stilbene synthase of Cenchrus americanus in complex with coenzyme A
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 10 %(v/v) Glycerol, 0.9 M Sodium Citrate Tribasic pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.66 66.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.864 α = 90 b = 137.304 β = 90 c = 179.173 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 1.43 90.5 93.4 0.965 6.4 9.8 218886
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 1.43 1.51 89.1 0.374 0.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.435 90.5 207794 10481 88.69 0.176 0.1751 0.1757 0.1992 0.1999 24.088
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] -0.515 -0.327 0.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.433 r_lrange_it 15.648 r_lrange_other 15.111 r_dihedral_angle_3_deg 12.935 r_scangle_it 12.756 r_scangle_other 12.754 r_scbond_it 8.906 r_scbond_other 8.905 r_mcangle_other 7.892 r_mcangle_it 7.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.433 r_lrange_it 15.648 r_lrange_other 15.111 r_dihedral_angle_3_deg 12.935 r_scangle_it 12.756 r_scangle_other 12.754 r_scbond_it 8.906 r_scbond_other 8.905 r_mcangle_other 7.892 r_mcangle_it 7.885 r_dihedral_angle_2_deg 7.839 r_dihedral_angle_1_deg 6.254 r_mcbond_it 5.652 r_mcbond_other 5.622 r_rigid_bond_restr 4.171 r_angle_refined_deg 1.867 r_angle_other_deg 0.635 r_nbd_refined 0.225 r_nbd_other 0.214 r_symmetry_nbd_refined 0.202 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.076 r_dihedral_angle_other_2_deg 0.03 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6043 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing