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SbSOMT in complex with resveratrol and nicotinamide adenine dinucleotide(NAD+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other MrBUMP generated chimeric model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.1 M sodium acetate pH 4.6, 0.2 M sodium acetate , 0.2 M ammonium chloride, 2.5% (w/v) polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.74 55.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.831 α = 90 b = 96.831 β = 90 c = 168.038 γ = 120
Symmetry Space Group P 31 2 1
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 PSI PILATUS 6M 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.72 48.462 99.8 0.06 0.063 0.02 1 30.2 19.4 97225 22.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 97.1 0.941 1.01 0.357 0.849 2.9 14.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MrBUMP generated chimeric model 1.72 48.462 97159 4899 99.826 0.165 0.1633 0.1763 0.1893 0.1981 26.372
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] -0.735 -0.367 -0.735 2.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.817 r_dihedral_angle_6_deg 15.67 r_dihedral_angle_3_deg 14.638 r_lrange_it 8.15 r_lrange_other 8.107 r_dihedral_angle_1_deg 6.362 r_scangle_it 6.057 r_scangle_other 6.057 r_scbond_it 4.125 r_scbond_other 4.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.817 r_dihedral_angle_6_deg 15.67 r_dihedral_angle_3_deg 14.638 r_lrange_it 8.15 r_lrange_other 8.107 r_dihedral_angle_1_deg 6.362 r_scangle_it 6.057 r_scangle_other 6.057 r_scbond_it 4.125 r_scbond_other 4.125 r_mcangle_it 3.93 r_mcangle_other 3.929 r_mcbond_it 2.816 r_mcbond_other 2.816 r_angle_refined_deg 1.639 r_angle_other_deg 0.558 r_nbd_refined 0.225 r_nbd_other 0.217 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.176 r_symmetry_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.164 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5622 Nucleic Acid Atoms Solvent Atoms 568 Heterogen Atoms 229
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing BUCCANEER phasing