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SbSOMT in complex with pinostilbene and nicotinamide adenine dinucleotide(NAD+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VB8
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 2.71 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.7 α = 90 b = 96.7 β = 90 c = 166.9 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 2021-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9784 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 2.101 19.712 99.8 0.218 0.238 0.094 0.891 9.2 6.4 53180 31.43
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 2.101 2.14 99 0.724 0.788 0.31 0.79 2 6.5
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 7VB8 2.101 19.712 53133 2652 99.67 0.172 0.1708 0.1818 0.2025 0.2109 34.983
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] -0.495 -0.248 -0.495 1.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.335 r_dihedral_angle_3_deg 16.121 r_dihedral_angle_2_deg 12.256 r_lrange_other 10.505 r_lrange_it 10.501 r_scangle_it 8.856 r_scangle_other 8.855 r_dihedral_angle_1_deg 7.28 r_scbond_it 6.298 r_scbond_other 6.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.335 r_dihedral_angle_3_deg 16.121 r_dihedral_angle_2_deg 12.256 r_lrange_other 10.505 r_lrange_it 10.501 r_scangle_it 8.856 r_scangle_other 8.855 r_dihedral_angle_1_deg 7.28 r_scbond_it 6.298 r_scbond_other 6.297 r_mcangle_it 5.995 r_mcangle_other 5.995 r_mcbond_it 4.498 r_mcbond_other 4.495 r_angle_refined_deg 2.023 r_angle_other_deg 0.677 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_other 0.235 r_nbd_refined 0.223 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_other 0.173 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5616 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 274
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing