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Design, synthesis, and X-ray of selenides bearing benzenesulfonamide moiety with neuropathic pain modulating effects
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 8.6 281 200 nL 7 mg/mL protein + 200 nL reservoir (2.8 M ammonium sulfate, 100 mM Tris, pH 8.6)
Crystal Properties Matthews coefficient Solvent content 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.327 α = 90 b = 41.341 β = 104.43 c = 72.08 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 2017-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 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 1.4 69.8 100 0.177 0.048 0.998 11.8 14.5 47834
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 1.4 1.42 100 1.231 0.395 0.723 2.1 10.5
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 (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 1.4 69.8 45559 2240 99.96 0.16235 0.16144 0.1688 0.18077 0.1863 RANDOM 9.525
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] -0.28 0.06 -0.07 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.281 r_dihedral_angle_4_deg 20.354 r_dihedral_angle_3_deg 11.692 r_dihedral_angle_1_deg 6.333 r_long_range_B_refined 3.206 r_long_range_B_other 3.206 r_scangle_other 1.479 r_angle_refined_deg 1.431 r_mcangle_it 1.092 r_mcangle_other 1.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.281 r_dihedral_angle_4_deg 20.354 r_dihedral_angle_3_deg 11.692 r_dihedral_angle_1_deg 6.333 r_long_range_B_refined 3.206 r_long_range_B_other 3.206 r_scangle_other 1.479 r_angle_refined_deg 1.431 r_mcangle_it 1.092 r_mcangle_other 1.092 r_scbond_it 0.923 r_scbond_other 0.923 r_angle_other_deg 0.759 r_mcbond_it 0.645 r_mcbond_other 0.644 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 2064 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing