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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 DROP PLATES WITH 200 NL PROTEIN AT 5 MG/ML AND 200 NL RESERVOIR WITH 2.6 TO 2.8 M AMMONIUM SULFATE AND 100 MM TRIS AT PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.885 α = 90 b = 41.263 β = 104.19 c = 71.681 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 1.28 41.3 97.4 0.07 15.8 7.3 59861
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 1.28 1.3 90.6 0.69 2.3 6.5
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 5A6H 1.28 69.5 57012 2842 97.43 0.13143 0.12992 0.1387 0.1631 0.1721 RANDOM 13.377
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] 0.41 -0.11 -0.27 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.496 r_sphericity_free 32.026 r_dihedral_angle_4_deg 17.637 r_dihedral_angle_3_deg 12.032 r_sphericity_bonded 9.16 r_dihedral_angle_1_deg 6.943 r_rigid_bond_restr 3.985 r_long_range_B_refined 3.734 r_long_range_B_other 3.733 r_scangle_other 2.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.496 r_sphericity_free 32.026 r_dihedral_angle_4_deg 17.637 r_dihedral_angle_3_deg 12.032 r_sphericity_bonded 9.16 r_dihedral_angle_1_deg 6.943 r_rigid_bond_restr 3.985 r_long_range_B_refined 3.734 r_long_range_B_other 3.733 r_scangle_other 2.223 r_scbond_it 1.733 r_scbond_other 1.732 r_angle_refined_deg 1.566 r_mcangle_other 1.349 r_mcangle_it 1.279 r_angle_other_deg 1.12 r_mcbond_it 0.889 r_mcbond_other 0.878 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2055 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing