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Synthesis of novel seleno ureido containing compounds as SLC-0111 analogs. Investigations on carbonic anhydrases activity, glutathione peroxidase and X-ray crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 concentrated CA II at ~10 mg/mL was set up in SD-2 plates (Molecular Dimensions) with the following ratio of protein plus reservoir plus
seeds: 250 nL + 225 nL + 25 nL. The plate was incubated at 8 C and the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1
M Tris buffer at pH 8.3. Dry compound was added to the crystallization drop after crystals had formed and several days before data were
collected.
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.485 α = 90 b = 41.498 β = 104.42 c = 72.28 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 210 2016-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 1.00800 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 41.5 99.3 0.225 0.112 0.978 5.7 5 13493
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 92.4 0.793 0.396 0.755 2 4.8
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 4cq0 2.15 41.5 12801 680 99.29 0.19944 0.19628 0.2041 0.26112 0.2636 RANDOM 20.219
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] -1.04 0.42 -2.36 2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.798 r_dihedral_angle_4_deg 20.734 r_dihedral_angle_3_deg 16.081 r_dihedral_angle_1_deg 6.949 r_long_range_B_refined 4.269 r_long_range_B_other 4.269 r_scangle_other 2.564 r_mcangle_other 2.155 r_mcangle_it 2.154 r_angle_refined_deg 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.798 r_dihedral_angle_4_deg 20.734 r_dihedral_angle_3_deg 16.081 r_dihedral_angle_1_deg 6.949 r_long_range_B_refined 4.269 r_long_range_B_other 4.269 r_scangle_other 2.564 r_mcangle_other 2.155 r_mcangle_it 2.154 r_angle_refined_deg 1.658 r_scbond_other 1.575 r_scbond_it 1.573 r_mcbond_it 1.331 r_mcbond_other 1.328 r_angle_other_deg 1 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing