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An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A6H PDB ENTRY 5A6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 SITTING DROPS WITH 150 NL PROTEIN AT 5.5 MG/ML WITH 120 NL RESERVOIR AND 30 NL SEEDS. THE RESERVOIR HAD 2.6 TO 2.8 M AMMONIUM SULFATE WITH 100 MM TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.706 α = 90 b = 41.286 β = 104.19 c = 72.13 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 CCD 2015-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 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 1.55 41.3 98 0.08 15.8 7.5 34094
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 1.55 1.58 95.7 0.72 2.6 7.2
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 5A6H 1.55 69.93 32405 1675 97.73 0.13473 0.13248 0.1428 0.17851 0.1898 RANDOM 16.503
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] -0.37 0.41 -0.32 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.407 r_sphericity_free 21.591 r_dihedral_angle_4_deg 17.521 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 6.809 r_sphericity_bonded 5.844 r_rigid_bond_restr 2.074 r_angle_refined_deg 1.658 r_scbond_it 1.572 r_mcangle_it 1.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.407 r_sphericity_free 21.591 r_dihedral_angle_4_deg 17.521 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 6.809 r_sphericity_bonded 5.844 r_rigid_bond_restr 2.074 r_angle_refined_deg 1.658 r_scbond_it 1.572 r_mcangle_it 1.306 r_mcbond_it 1.102 r_mcbond_other 1.074 r_angle_other_deg 0.988 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2045 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing