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SbSOMT in complex with pterostilbene 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 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.469 α = 90 b = 96.469 β = 90 c = 169.43 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 2.401 31.421 99.8 0.199 0.204 0.046 0.915 7.5 19.5 36363 36.78
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 2.401 2.44 99.9 0.955 0.982 0.228 0.871 0.8 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 2.401 31.421 36012 1899 99.138 0.19 0.1873 0.1944 0.2462 0.2497 43.738
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] -0.756 -0.378 -0.756 2.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.674 r_dihedral_angle_6_deg 15.666 r_dihedral_angle_2_deg 13.217 r_lrange_other 12.921 r_lrange_it 12.92 r_scangle_it 10.395 r_scangle_other 10.393 r_mcangle_it 8.495 r_mcangle_other 8.494 r_dihedral_angle_1_deg 7.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.674 r_dihedral_angle_6_deg 15.666 r_dihedral_angle_2_deg 13.217 r_lrange_other 12.921 r_lrange_it 12.92 r_scangle_it 10.395 r_scangle_other 10.393 r_mcangle_it 8.495 r_mcangle_other 8.494 r_dihedral_angle_1_deg 7.863 r_scbond_it 7.747 r_scbond_other 7.745 r_mcbond_other 6.149 r_mcbond_it 6.148 r_angle_refined_deg 1.993 r_angle_other_deg 0.651 r_symmetry_xyhbond_nbd_other 0.257 r_nbd_other 0.25 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.215 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.179 r_ncsr_local_group_1 0.129 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_refined 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5622 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing