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Design, Synthesis, X-ray and Biological Activities of Selenides Bearing the Benzenesulfonamide Moiety as New Class of Agents for Prevention of Diabetic Cerebrovascular Pathology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CQ0 PDB ENTRY 4CQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 200 nL 7 mg/mL protein + 200 nL reservoir solution (2.9 M ammonium sulfate, 100 mM Tris buffer, pH 8.3), equilibriated at 281K
Crystal Properties Matthews coefficient Solvent content 2.11 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.452 α = 90 b = 41.485 β = 104.49 c = 72.455 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 210r 2017-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.43 41.5 99.3 0.092 17.1 7.1 45001
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.46 95.9 0.59 3.3 6.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4CQ0 1.43 41.5 42805 2100 99.1 0.155 0.152 0.1524 0.208 0.2077 RANDOM 11.03
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] -0.26 0.11 -0.11 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.613 r_sphericity_free 22.796 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 11.285 r_sphericity_bonded 8.268 r_dihedral_angle_1_deg 6.651 r_long_range_B_refined 2.992 r_long_range_B_other 2.992 r_rigid_bond_restr 2.493 r_scangle_other 2.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.613 r_sphericity_free 22.796 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 11.285 r_sphericity_bonded 8.268 r_dihedral_angle_1_deg 6.651 r_long_range_B_refined 2.992 r_long_range_B_other 2.992 r_rigid_bond_restr 2.493 r_scangle_other 2.309 r_scbond_it 2.027 r_scbond_other 1.974 r_angle_refined_deg 1.916 r_mcangle_other 1.517 r_mcangle_it 1.505 r_mcbond_it 1.266 r_mcbond_other 1.249 r_angle_other_deg 1.057 r_chiral_restr 0.131 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing