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Stilbene synthase of Cenchrus americanus in apo form
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% Glycerol, 0.9 M sodium citrate tribasic pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.7 66.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.915 α = 90 b = 138.194 β = 90 c = 179.791 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 1.41 109.57 99.7 0.997 9.9 13.4 250737 15
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 1.41 1.48 99.3 0.993 1.1 13.4
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 1.41 109.567 250356 12223 99.549 0.178 0.1772 0.1849 0.1899 0.199 21.862
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] -0.704 0.203 0.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.053 r_dihedral_angle_3_deg 12.98 r_dihedral_angle_2_deg 8.305 r_lrange_it 6.617 r_lrange_other 6.571 r_dihedral_angle_1_deg 6.492 r_scangle_it 5.559 r_scangle_other 5.558 r_scbond_it 3.645 r_scbond_other 3.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.053 r_dihedral_angle_3_deg 12.98 r_dihedral_angle_2_deg 8.305 r_lrange_it 6.617 r_lrange_other 6.571 r_dihedral_angle_1_deg 6.492 r_scangle_it 5.559 r_scangle_other 5.558 r_scbond_it 3.645 r_scbond_other 3.645 r_mcangle_it 2.92 r_mcangle_other 2.92 r_mcbond_it 2.079 r_angle_refined_deg 2.067 r_mcbond_other 2.064 r_angle_other_deg 0.667 r_symmetry_nbd_refined 0.307 r_nbd_refined 0.224 r_nbd_other 0.224 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.181 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.084 r_gen_planes_other 0.016 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6043 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing