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SbSOMT in complex with resveratrol
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 291 0.1 M MES pH 6.5, 0.2 M ammonium sulphate, 30% (w/v) polyethylene glycol monomethyl ether 5000
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.485 α = 90 b = 111.733 β = 90 c = 131.102 γ = 90
Symmetry Space Group P 21 21 21
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 0.978530 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 2.55 48.956 99.9 0.118 0.127 0.048 0.999 16.3 13.2 46864 52.2
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 2.56 2.65 100 1.156 1.247 0.468 0.902 2.4 13.6
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 7VB8 2.56 48.956 46802 2368 99.932 0.19 0.1864 0.1942 0.2567 0.2585 65.847
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] -6.587 0.516 6.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.694 r_dihedral_angle_3_deg 19.332 r_dihedral_angle_6_deg 15.446 r_lrange_it 12.62 r_lrange_other 12.62 r_scangle_it 10.459 r_scangle_other 10.458 r_mcangle_it 9.851 r_mcangle_other 9.851 r_dihedral_angle_1_deg 8.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.694 r_dihedral_angle_3_deg 19.332 r_dihedral_angle_6_deg 15.446 r_lrange_it 12.62 r_lrange_other 12.62 r_scangle_it 10.459 r_scangle_other 10.458 r_mcangle_it 9.851 r_mcangle_other 9.851 r_dihedral_angle_1_deg 8.285 r_scbond_it 7.85 r_scbond_other 7.849 r_mcbond_it 7.051 r_mcbond_other 7.05 r_angle_refined_deg 2.381 r_angle_other_deg 0.79 r_nbd_refined 0.238 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.189 r_nbd_other 0.188 r_symmetry_nbd_refined 0.182 r_xyhbond_nbd_refined 0.18 r_symmetry_xyhbond_nbd_other 0.142 r_ncsr_local_group_5 0.139 r_ncsr_local_group_3 0.138 r_ncsr_local_group_4 0.138 r_ncsr_local_group_2 0.135 r_ncsr_local_group_1 0.133 r_ncsr_local_group_6 0.13 r_symmetry_xyhbond_nbd_refined 0.119 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11270 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing