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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 8.5 200 NL PLUS 200 NL OF PROTEIN AT 5 MGS/ML AND RESERVOIR IN SITTING DROP PLATES. RESERVOIR WAS 2.6 TO 2.8 M AMMONIUM SULFATE WITH 100 MM TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.159 α = 90 b = 41.494 β = 104.26 c = 71.699 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 1.4 41.5 99 0.07 14.1 7.2 47179
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 1.4 1.42 84.7 0.74 2.2 6.3
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 1.4 69.49 44950 2214 99.04 0.12977 0.1281 0.1386 0.16534 0.1749 RANDOM 16.176
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] 0.33 0.1 -0.14 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.478 r_sphericity_free 32.69 r_dihedral_angle_4_deg 19.457 r_dihedral_angle_3_deg 12.653 r_sphericity_bonded 9.619 r_rigid_bond_restr 8.294 r_dihedral_angle_1_deg 6.891 r_scbond_it 2.484 r_angle_refined_deg 1.718 r_mcangle_it 1.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.478 r_sphericity_free 32.69 r_dihedral_angle_4_deg 19.457 r_dihedral_angle_3_deg 12.653 r_sphericity_bonded 9.619 r_rigid_bond_restr 8.294 r_dihedral_angle_1_deg 6.891 r_scbond_it 2.484 r_angle_refined_deg 1.718 r_mcangle_it 1.715 r_mcbond_it 1.296 r_mcbond_other 1.273 r_angle_other_deg 1.145 r_chiral_restr 0.102 r_bond_refined_d 0.012 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 2055 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing