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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 8.3 281 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 c
ollected.
Crystal Properties Matthews coefficient Solvent content 2.11 41.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.489 α = 90 b = 41.563 β = 104.48 c = 72.203 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 1.35 41.6 94 0.042 0.017 1 31.3 7.3 50449
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 1.35 1.37 61.5 0.284 0.124 0.948 6.3 6.1 1628
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 1.35 41.6 48038 2395 93.7 0.10738 0.10571 0.1056 0.14261 0.1425 RANDOM 13.843
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] 0.17 -0.07 0.06 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_sphericity_free 23.406 r_dihedral_angle_4_deg 21.597 r_dihedral_angle_3_deg 12.649 r_sphericity_bonded 9.972 r_dihedral_angle_1_deg 6.33 r_long_range_B_refined 3.271 r_long_range_B_other 3.27 r_scangle_other 2.904 r_rigid_bond_restr 2.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_sphericity_free 23.406 r_dihedral_angle_4_deg 21.597 r_dihedral_angle_3_deg 12.649 r_sphericity_bonded 9.972 r_dihedral_angle_1_deg 6.33 r_long_range_B_refined 3.271 r_long_range_B_other 3.27 r_scangle_other 2.904 r_rigid_bond_restr 2.856 r_scbond_other 2.602 r_scbond_it 2.601 r_mcangle_other 1.896 r_mcangle_it 1.878 r_angle_refined_deg 1.783 r_mcbond_it 1.484 r_mcbond_other 1.469 r_angle_other_deg 1.034 r_chiral_restr 0.124 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 327 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing